Full opinion text
MEMORANDUM OPINION KOLLAR-KOTELLY, District Judge. This is the second time that the Court has been presented with cross-motions for summary judgment during the unusual procedural history of this APA litigation. Plaintiff Hawaii Longline Association’s (“HLA’s”) Second Amended Complaint seeks to set aside regulations and a biological opinion issued by Defendants National Marine Fisheries Service (“NMFS”) and Secretary Donald L. Evans affecting the Fishery Management Plan for the Western Pacific Region. Specifically, HLA has moved for summary judgment regarding its second claim for relief, which challenges a rule promulgated on June 12, 2002, 67 Fed.Reg. 40,232 (June 12, 2002) (“June 2002 Regulations”). It has also requested judgment in its favor regarding its third claim for relief, which contests a Biological Opinion issued on November 15, 2002 (“2002 BiOp”). After due consideration of the parties’ motions, their oppositions, and their replies, the Court shall grant Plaintiffs Motion for Summary Judgment regarding its second and third claims for relief and deny Defendants’ Cross-Motions. With no material facts in dispute, the Court has determined that the June 2002 Regulations and the 2002 BiOp are arbitrary, capricious, and contrary to law and, therefore, shall be vacated and remanded to NMFS as a matter of law. I. BACKGROUND The issues in this case arise at the cross section of two discrete federal statutes, the Magnuson-Stevens Act, 16 U.S.C. § 1801 et seq., and the Endangered Species Act, 16 U.S.C. § 1531 et seq. Therefore, it is necessary to briefly consider the authority NMFS derives from each statute before reviewing the events leading up to the present motions before the Court. After reviewing the statutory framework under which NMFS operates, the Court will then sketch out the events that have transpired in this complicated administrative law ease. (A) Statutory Framework (1) The Magnuson-Stevens Fishery Conservation and Management Act Fisheries under the jurisdiction of the United States are regulated by the Mag-nuson-Stevens Fishery Conservation and Management Act (“Magnuson-Stevens Act”), 16 U.S.C. § 1801 et seq. Among its various provisions, the Magnuson-Stevens Act established eight regional councils comprised of “individuals who, by reason of their occupational or other experience, scientific expertise, or training, are knowledgeable regarding conservation and management, or the commercial or recreational harvest, of the fishery resources of the geographical area concerned.” 16 U.S.C. § 1852(a)(2)(A). In order to ensure a balanced cross-section of interested parties on each council, the Act requires the Secretary of Commerce — and, ultimately NMFS — to abide by certain appointment and reporting requirements. 16 U.S.C. § 1852(a)(2)(B). Each council is vested with the authority to issue regulations for the conservation and management of the fisheries in its geographic region, including comprehensive Fishery Management Plans (“FMPs”). 16 U.S.C. § 1853(a), (c). The proposals of the regional councils are subject to review by NMFS, which must examine each submission to ensure that it is consistent with the requirements under the Act. See 16 U.S.C. § 1854(a), (b). These substantive requirements demand that an FMP be “necessary and appropriate for the conservation and management of the fishery,” 16 U.S.C. § 1853(a)(1)(A), be consistent with national standards set out in the Act, 16 U.S.C. § 1853(a)(1)(C), and abide by “any other applicable law,” id., including the Endangered Species Act. In certain situations, NMFS may prepare an FMP without the input of the appropriate regional council via a “Secretarial amendment.” However, the statute limits such situations, granting such authority only where: (A) the appropriate Council fails to develop and submit to the Secretary, after a reasonable period of time, a fishery management plan for such fishery, or any necessary amendment to such a plan, if such fishery requires conservation and management; (B) the Secretary disapproves or partially disapproves any such plan or amendment, or disapproves a revised plan or amendment, and the Council involved fails to submit a revised or further revised plan or amendment; or (C) the Secretary is given authority to prepare such a plan under this section. 16 U.S.C. § 1854(c)(1). In addition, NMFS may promulgate emergency regulations or interim measures (through the Secretary) in the event that “an emergency exists or [where] interim measures are necessary to reduce overfishing for any industry.” 16 U.S.C. § 1855(c)(1). Regulations promulgated by NMFS (through the Secretary) pursuant to its emergency powers are limited in duration and may not exceed 180 days, but may be extended for an additional 180-day period, subject to the requirements of the Act. 16 U.S.C. § 1855(c)(3)(B). The fisheries based in Hawaii, American Samoa, Guam, and the Northern Mariana Islands fall under the authority of the Western Pacific Fishery Management Council (“West Pac” or “the Council”). 16 U.S.C. § 1852(a)(1)(H). As a result, under the Magnuson-Stevens Act, West Pac is responsible for issuing various FMPs, including the Pelagics (Open Ocean) FMP central to the dispute in the present case. (2) The Endangered Species Act The Endangered Species Act (“ESA”), 16 U.S.C. § 1531 et seq., establishes a comprehensive federal program to limit the number of fish, wildlife, and plant species rendered extinct as a consequence of their interactions with mankind. Under the ESA, the U.S. Fish and Wildlife Service (“FWS”) and NMFS (collectively, “the Services”) are required to promulgate regulations listing those species that are “threatened” or “endangered” based on enumerated criteria and to “designate any habitat of such species which is then considered to be critical habitat.” 16 U.S.C. § 1533. The ESA further requires that each federal agency, in consultation with the Services, “insure that any action authorized, funded, or carried out by such agency ... is not likely to jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of habitat of such species which is determined by [the Services]... to be critical.” 16 U.S.C. § 1536(a)(1). Under the ESA and its implementing regulations, a federal agency must engage in formal consultation with the Services if an action undertaken by that agency “may affect” an endangered or threatened species or its critical habitat. 50 C.F.R. § 402.14(a). In the event that formal consultation is required, the appropriate consulting Service (in this case, NMFS) will review the proposed agency action by undertaking a Biological Opinion (“BiOp”). 50 C.F.R. § 402.14(g). The BiOp considers and details how the proposed agency action affects any listed species or its critical habitat. In making this inquiry, the Service must comport with the statute’s “best science” requirement. 16 U.S.C. § 1536(a)(2); 50 C.F.R. § 402.14(h). This comprehensive review of the agency’s action generally leads to one of two possible results: (1) the action either “jeopardizes” or (2) does not jeopardize the listed species. 50 C.F.R. § 402.14(h)(3). When the consulting Service determines that an agency action is likely to jeopardize a protected species, it must provide “reasonable and prudent alternatives” (“RPAs”) that would not jeopardize the listed species. 16 U.S.C. § 1536(b)(3)(A); 50 C.F.R. § 402. An RPA represents an alternative means to implement a proposed action, and would accomplish the same general purpose of the proposed action, without jeopardizing the listed species. On the other hand, if the consulting Service reaches a “no jeopardy” conclusion, or if an RPA is available that would avoid jeopardy, the Service issues an Incidental Take Statement. 16 U.S.C. § 1536(b)(4); 50 C.F.R. § 402.14(i). An Incidental Take Statement permits an agency to undertake an action that leads to the “taking” (harassment, injury, or death) of a particular number of listed species without violating the ESA’s taking prohibitions. 16 U.S.C. § 1536(b)(4); 50 C.F.R. § 402.14(i). If one of the Services issues an Incidental Take Statement, the agency undertaking the proposed action (“action agency”) is required to reinitiate consultations with one of the consulting Services where the action agency retains discretionary involvement over the action or control of the action has been retained or is authorized by a federal statute and: (a) If the amount or extent of taking specified in the incidental take statement is exceeded; (b) If new information reveals effects of the action that may affect listed species or critical habitat in a manner or to an extent not previously considered; (c) If the identified action is subsequently modified in a manner that causes an effect to the listed species or critical habitat that was not considered in the biological opinion; or (d) If a new species is listed or critical habitat designated that may be affected by the identified action. 50 C.F.R. § 402.16. In the event that an action agency determines that it must rein-itiate formal consultations with a consulting Service, that Service will issue a new biological opinion evaluating the proposed agency action. (3) Dual Responsibilities In the unique situation presented by this case, NMFS is responsible for authorizing regulations and FMPs proposed by the eight regional councils under the Magnu-son-Stevens Act but, at the same time, must evaluate its own actions under the ESA. In other words, NMFS serves as both the action agency and the consulting Service. See, e.g., 2001 BiOp AR-604, at 9099 (listing the National Marine Fisheries Service, Southwest Region Sustainable Fisheries Division as the action agency and the National Marine Fisheries Service, Endangered Species Division as the consulting Service). In the context of the instant matter, this means that NMFS must approve amendments to the existing Pelagics FMP, but because the FMP could affect the listed turtles, NMFS must also issue a BiOp to determine if the FMP jeopardizes the listed turtles. (B) Factual Background At the outset, the Court observes that the United States District Court for the District of Columbia has supplemented Federal Rule of Civil Procedure 56 with Local Civil Rule 56.1, which requires that each party submitting a motion for summary judgment attach a statement of material facts to which that party contends there is no genuine issue, with specific citations to those portions of the record upon which the party relies in fashioning the statement. The party opposing such a motion must, in turn, submit a statement of genuine issues enumerating all material facts which the party contends are at issue and thus require litigation. See LCvR 56.1. Where the opposing party fails to discharge this obligation, a court may take all facts alleged by the movant as admitted. Id. As this Circuit has emphasized, “[LCvR 56.1] places the burden on the parties and their counsel, who are most familiar with the litigation and the record, to crystallize for the district court the material facts and relevant portions of the record.” Jackson v. Finnegan, Henderson, Farabow, Garrett & Dunner, 101 F.3d 145, 151 (D.C.Cir.1996) (citing Twist v. Meese, 854 F.2d 1421, 1425 (D.C.Cir.1988); Guarino v. Brookfield Township Trustees, 980 F.2d 399, 406 (6th Cir.1992)). Because of the significance of this task and the potential hardship placed on the court if parties are derelict in their duty, courts require strict compliance with LCvR 56.1. See id. at 150 (citations omitted). This Court strictly adheres to the text of Local Civil Rule 56.1 when resolving motions for summary judgment. See HLA v. NMFS, Civ. No. 01-0765 (D.D.C. Nov. 28, 2001) (order denying HLA’s motion for relief from LCvR 56.1); see also Burke v. Gould, 286 F.3d 513, 519 (D.C.Cir.2002) (holding that district courts need to invoke Local Civil Rule 56.1 before applying it to the case). Although discretionary by the text of the Local Civil Rules, in resolving the present summary judgment motions, this Court “assumes that facts identified by the moving party in its statement of material facts are admitted, unless such a fact is controverted in the statement of genuine issues filed in opposition to the motion.” LCvR 56.1. For purposes of this opinion, the Court primarily cites to the Administrative Record. In instances where an issue is raised regarding a material fact, the Court has reviewed the record citations by the parties to ensure that the parties’ characterizations of the record are accurate. In addition, due to the complicated nature of this administrative law case, the Court must consider the procedural history of prior litigation between these parties. In some instances, relevant decisions in this prior case were cited in the parties’ pleadings, but not contained in their Statements of Material Facts Not in Genuine Dispute. Therefore, the Court will use its discretion under Local Civil Rule 56.1 to consider this material outside the Statements provided by the parties. Having set forth these preliminaries, the Court moves to a discussion of the material facts not genuinely in dispute. (1) Endangered and Threatened Sea Turtles, the Fishery, and the 1998 BiOp The five species of sea turtles implicated in these proceedings — and all sea turtles for that matter — are listed as endangered or threatened under the ESA. See 50 C.F.R. § 17.11. It is beyond dispute that, incidental to catching desired commercial fish, such as swordfish and tuna, the long-line fishing industry (“the Fishery”) kills or injures sea turtles each year. 2001 BiOp AR-604, at 9184-202. For example, sea turtles may become entangled or hooked by the Fishery’s gear, which can mortally wound, severely injury, or drown the turtles. Id. at 9184. The Fishery is regulated by the Western Pacific Pelagics FMP (“Pelagics FMP”), which was implemented in 1987 under the authority of the Magnuson-Stevens Act, 52 Fed.Reg. 5,987 (Mar. 23, 1987). Id. at 9263; 2001 BiOp AR-138, at 3167. The Pelagics FMP replaced a preliminary FMP prepared by NMFS on behalf of the Secretary of Commerce in 1980. 2001 BiOp AR-604, at 9263. Since the Pelagics FMP was first issued, it has been revised and amended. 2001 BiOp AR-138, at 3167-68. In 1998, NMFS reinitiated consultations for the Pelagics FMP under the ESA, id. at 3164, because the anticipated incidental take statement in a prior BiOp had been exceeded, id. at 3171. These formal consultations produced the November 3, 1998, BiOp (“1998 BiOp”), which found that the Fishery, operating under the existing Pelagics FMP, was “not likely to jeopardize the continued existence and recovery of loggerhead, leatherback, olive ridley, green or hawksbill turtles or adversely modify critical habitat.” Id. at 3164. Therefore, based on its no jeopardy conclusion, the 1998 BiOp established Incidental Take Statement levels for sea turtles captured, injured, or killed by the Fishery. Id. at 3165; 2001 BiOp AR-604, at 9101. (2) CMC Litigation and the Decision to Reinitiate Consultations In 1999, several environmental advocacy groups filed suit against NMFS in the United States District Court for the District of Hawaii, Center for Marine Conservation v. NMFS (“CMC”), Civ. No. 99-00152 (D.Haw.2000), challenging the above-mentioned 1998 BiOp under the ESA and the National Environmental Policy Act (“NEPA”), 42 U.S.C. § 4331, et seg. The plaintiffs in that case disputed the 1998 BiOp’s no jeopardy finding. Nonetheless, the court upheld the no jeopardy conclusion reached in the 1998 BiOp. CMC, Civ. No. 99-00152, slip op. at 16-31 (Oct. 18, 1999). At the same time, it granted a limited injunction pending the completion of an Environmental Impact Statement (“EIS”) as required by NEPA. Id. at 41-42. According to the court, an Environmental Assessment-the potential precursor to an EIS — has a “different purpose! ] from [a] biological opinion! ]. A ‘no jeopardy’ finding in the [1998] biological opinion cannot be compared to a ‘Finding of No Significant Impact’ which is what may or may not have been determined had Defendants prepared an Environmental Assessment.” Id. at 37. Therefore, having determined that the plaintiffs had established both a likelihood of success on the merits and irreparable harm, the court reasoned that an injunction was appropriate because it “ ‘is the most common judicial response to a NEPA violation ... [, and it] ... maintains] the status quo while additional environmental data is obtained.’ ” Id. at 39 (quoting Forelaws on Board v. Johnson, 743 F.2d 677, 685 (9th Cir.1984)). The court refused to completely enjoin the Fishery’s activities, but determined that “a carefully tailored injunction during the EIS preparation period [was] warranted.” The court also required NMFS to complete the EIS by April 1, 2001. 2002 Regulations AR-1, at 5. On May 18, 2000, concurrent with the CMC litigation, NMFS determined that the Fishery “had likely exceeded anticipated incidental take levels for olive ridley turtles” based on the levels set by the 1998 BiOp.2001 BiOp AR-604, at 9101. As a result, on June 7, 2000, NMFS reinitiated formal consultation as required under the ESA and the Services’ implementing regulations. Id.; 16 U.S.C. § 1539; 50 C.F.R. § 402.16. This formal consultation would produce the March 29, 2001, BiOp (2001 BiOp) that originally prompted this litigation. Accordingly, following the decision to reinitiate formal consultations, NMFS was engaged in two separate proceedings related to the Western Pacific Pelagics FMP: the development of the EIS, as ordered by the CMC court, and the 2001 BiOp. On August 25, 2000, NMFS promulgated an emergency interim rule to comply with the CMC court’s injunctive orders. 65 Fed. Reg. 51,992 (Aug. 25, 2000). Likewise, on December 22, 2000, NMFS published a Draft EIS, consistent with the order in the CMC litigation, and accepted comments until January 29, 2001. 65 Fed.Reg. 80,-828 (Dec. 22, 2000). At the same time, NMFS was preparing the 2001 BiOp, based on its decision to reinitiate consultations on June 7, 2000. 2001 BiOp AR-604, at 9101. On December 19, 2000, HLA counsel Jeffrey Leppo spoke with Judson Feder, NMFS Southwest Regional Counsel, over the telephone about obtaining a draft copy of the forthcoming 2001 BiOp.2001 BiOp AR-288, at 5628. It appears, based on a subsequent letter drafted by Leppo, that Feder indicated that “NMFS was unlikely to provide HLA with a draft version of the [BiOp] for review.” Id. Nonetheless, Lep-po persisted, formally lodging his request in a letter dated December 26, 2000. Id. at 5628-30. In the letter, Leppo argued that HLA was an “applicant” under the ESA and, therefore, was entitled to certain procedural rights under the statute and the Services’ implementing regulations; such as receiving a draft BiOp and providing comments. Id. On January 3, 2001, Feder indicated that the agency had rejected HLA’s request. 2001 BiOp AR-303, at 6262. (3) The 2001 BiOp and the Release of the Final EIS The final BiOp was published on March 29, 2001, 2001 BiOp AR-604, at 9097, but not before a contentious month during which the parties quarreled over the release of the Draft BiOp, the time provided for comment, and the consideration given by NMFS to those comments, 2001 BiOp AR-580, at 8999. The March 29, 2001, BiOp reversed the 1998 BiOp, concluding that the Fishery, operating under the existing Pelagics FMP, was likely to jeopardize the continued existence of the green, leatherback, and loggerhead turtles. 2001 BiOp AR-604, at 9097, 9099-100. In particular, the data in the 2001 BiOp suggested that the highest incidence of takings resulted from the use of swordfishing gear, while takes from tuna gear were limited to particular geographic areas. Id. at 9202-06. Accordingly, the 2001 BiOp included a RPA expected to avoid jeopardizing the listed turtles, id. at 9227-36, which would effectively prohibit fishing techniques targeted at swordfish and impose certain time and area closures for tuna fishing, id. at 9229-33. On the following day, March 30, 2001, NMFS released the Final EIS in compliance with the order issued by the CMC court. 2002 Regulations AR-1, at 1, 4. As required under NEPA, the Final EIS included “a reasonable range of alternative actions.” Id. at 17. In this case, ten possible alternatives were presented, ranging from complete deregulation of the Fishery to varying time and area closures. Id. at 18-19. The preferred alternative ultimately selected by NMFS was almost identical to the RPA announced just a day before in the 2001 BiOp: Both would (1) prohibit swordfish-style longline fishing methods by United States-based vessels north of the equator; (2) close areas south of 15 North latitude to the equator, bounded by 145 West and 180 longitude, to all U.S. longline vessels during the months of April and May of each year; and (3) impose certain permit registration restrictions. See id. at 126-29; 2001 BiOp AR-604, at 9229-32. As NMFS observed, however, “this EIS is not by itself a vehicle for the implementation of management regulations.... [T]he Magnuson-Stevens Act sets out a process, involving the Council and NMFS, to implement management actions.” 2002 Regulations AR-1, at 78. Although the terms of the preferred alternative were not self-executing — that is, NMFS had discretion to implement them through the West Pac Council — on March 30, 2001, the same day that the Final EIS was issued, the CMC court modified the terms of the injunctive order “in accordance with the findings in the EIS.” CMC, Civ. No. 99-00152 (D.Haw. Mar. 30, 2001) (order modifying injunction) at 2. The court noted that the purpose of its “earlier injunction was to preserve the status quo ... until an EIS could be prepared.” Id. Now that an EIS had been prepared, the court modified the terms of the injunction to reflect the preferred alternative in the EIS “until appropriate federal regulations [could] be enacted in accordance with law.” Id. (4) Initiation of the Present Litigation On April 10, 2001, HLA filed suit in the United States District Court for the District of Columbia. Its one count Complaint alleged that the 2001 BiOp was both procedurally and substantively flawed. Compl. ¶ 2. HLA sought, among other things, to have the 2001 BiOp vacated and remanded to NMFS, to review and comment on the preparation of a new BiOp, and to require that the completion of the new BiOp comply with a court-imposed schedule. Compl. at 20 (“Wherefore” Paragraphs). On June 6, 2001, several environmental advocacy groups, Turtle Island Restoration Network and the Ocean Conservancy (collectively “Defendant-Intervenors” or “Conservation Groups”) filed a motion to intervene pursuant to Federal Rule of Civil Procedure 24. The Conservation Groups, which originally initiated the CMC litigation, asserted an interest in the preservation of the sea turtles and the possible effect that this case could have on that interest. The Conservation Groups also filed their own lawsuit, challenging the 2001 BiOp as inadequate in the United States District Court for the District of Hawaii. Several days after the Conservation Groups moved to intervene, Defendants filed their Answer to Plaintiffs Complaint. Beyond responding to this litigation, however, NMFS was trying to implement the 2001 BiOp’s RPA. But to implement the RPA, NMFS would need the cooperation of West Pac, because, as discussed supra, in most instances the Council must approve an amendment to an FMP. Thus, shortly after Defendants filed their Answer, Rebecca Lent, NMFS Regional Administrator for the Southwest Region, sent a memorandum to Dr. William T. Hogarth, Acting Assistant Administrator for the Fisheries. In this memorandum, Lent stated: I believe that the [West Pac] Council is aware of NMFS’s obligation [under the ESA] to promulgate these measures but, if asked, I will explain that a Secretarial amendment to the Pelagics Fishery Management Plan will be required if the reasonable and prudent alternatives, and the terms and conditions of the biological opinion (also contained in the recently completed Final Environmental Impact Statement on this fishery), are not implemented via Council action. 2002 Regulations AR-2, at 1491 (emphasis added). Apparently, this message registered with the Council. In an internal West Pac memorandum, the Executive Director of the Council observed: The usual process for amending fishery management measures under an FMP is to develop a series of alternative measures for consideration, and through public meeting, and meetings of the Council narrow the selection to a preferred alternative. This regulatory amendment is different in that the Council is obliged to implement the preferred alternative of the March SOth 2001 FEIS, which is itself based on the March 29th 2001 BiOp. There are basically only two alternatives for the Council to consider. No action would force the Secretary of Commerce to impose these measures by a Secretarial amendment, or for the Council to amend the FMP and make it consistent with the FEIS preferred alternative and March 29th 2001 BiOp. Further its is [sic] critically important that the regulatory amendment be in place before June 2002, beyond which, the NMFS emergency rule cannot be extended. 2002 Regulations AR-19, at 1543 (emphasis added). However, at around the same time that West Pac noted the mandatory nature of the 2001 BiOp’s RPA, it also registered its “continued opposition” to the 2001 BiOp.2002 Regulations AR-3, at 1494. On June 12, 2001, NMFS promulgated additional emergency interim regulations, in essence, codifying the CMC court’s March 30, 2001, Order. 66 Fed.Reg. 31,-561 at 31,562 (June 12, 2001) (“The [CMC court’s] March 30, 2001, Order made effective immediately those aspects of the preferred alternative in the FEIS that are intended to mitigate the Hawaii longline fishery interactions with sea turtles. This emergency interim rule codifies that Order .... ”). As noted above, the preferred alternative in the Final EIS proffered remedies largely consistent with the RPA in the 2001 BiOp. Accordingly, the emergency interim rule adopted measures consistent with the 2001 BiOp. Id. Given the still pending injunction issued by the CMC court and the Hawaii court’s pre-existing familiarity with the underlying subject matter in this case, on June 11, 2001, the Court ordered the parties to show cause why this case should not be transferred to the United States District Court for the District of Hawaii. HLA v. NMFS, Civ. No. 01-765 (D.D.C. June 11, 2001) (order). Despite these factors, both parties opposed transferring the case, and the Court acknowledged that ordering a transfer, sua sponte, “ ‘should be reserved for exceptional circumstances.’” HLA v. NMFS, No. 01-765 (D.D.C. Aug. 7, 2001) (order preserving venue and granting Defendants’ Motion for an Enlargement of Time) at 2 (quoting In re Scott, 709 F.2d 717, 721 (D.C.Cir.1983)). As a result, the Court decided that it was inappropriate to transfer the case. Id. On August 31, 2001, the Court ruled on the Conversation Groups’ motion to intervene, granting the motion in part and denying it in part. HLA v. NMFS, Civ. No. 01-0765, slip op. at 12 (D.D.C. Aug. 31, 2001) (“Intervention Op.”). Having noted that “courts need not consider a motion to intervene as an all-or-nothing proposition,” id. at 2 (citing Harris v. Pernsley, 820 F.2d 592, 599 (3d Cir.1987); see also Forest Conservation Council v. U.S. Forest Serv., 66 F.3d 1489, 1495-96 (9th Cir. 1995)), the Court granted the Conservation Groups’ motion as of right for the limited issue of defending the 2001 BiOp’s jeopardy conclusion, id. at 6. (5) Summary Judgment, West Pac Action, and Defendants’ Motion for a Stay With venue and intervention finally behind the Court, the parties began to brief their Cross-Motions for Partial Summary Judgment, with separate motions considering the procedural and substantive merits of the 2001 BiOp. Briefings on the procedural challenge were due first, followed by the substantive challenge. Around the time that the parties were briefing their Motions for Partial Summary Judgment, between October 23 and 26, 2001, West Pac met for its One Hundred and Eleventh Meeting of the Western Pacific Management Council. During that time, “[t]he Council took final action to recommend that the National Marine Fisheries Service (NMFS) implement the reasonable and prudent alternative contained in NMFS’ March 29, 2001, Biological Opinion concerning sea turtles.” 2002 Regulations AR-34, at 1720. On December 17, 2001, the same day that Defendants’ Opposition to the substantive Motion for Partial Summary Judgment was due, NMFS notified the Court of its decision to reinitiate consultations and issue a new BiOp. See Defs.’ Mot. for Partial Dismissal or, in the Alternative, for Stay of Proceedings Pending the Issuance of a New BiOp After Reiniti-ation of Consultation (“Defs.’ Mot. for Stay”) at 1. In support of their Motion, Defendants attached a memorandum from Rodney R. Mclnnis, Acting Regional Director of NMFS, which stated: new information is available which may improve NMFS’ ability to quantify and evaluate the effects of the United States’ pelagic fisheries and the reasonable and prudent alternatives in the BiOp on listed turtle populations. Therefore, ... NMFS is “reinitiating section 7 consultation under the Endangered Species Act (ESA) on the potential effects of the pelagic fisheries under the FMP on threatened and endangered species.” Id. Ex. A, at 1 (emphasis added) (also available at 2002 BiOp AR-114, at 821). The letter went on to note that “observer data since 1999 is available which may affect the estimated direct and indirect effects of the fisheries and the expected results of the reasonable and prudent alternative.” Id. Thus, NMFS made clear that it had “decided to reinitiate consultation and prepare a new biological opinion.” Defs.’ Mot. for Stay at 2; see also Defs.’ Reply, Mot. for Stay at 2 (stating that “the 2001 BiOp has limited continuing applicability and will soon be superceded ”) (emphasis added); id. at 3 (arguing that “the imminent issuance of a new biological opinion renders litigation and judicial analysis of the 2001 BiOp imprudent ”) (emphasis added). Based on this representation, and given the fact that the 2001 BiOp would be “superceded” by the new BiOp, the Court determined that the most prudent course would be to resolve Plaintiffs procedural claims against NMFS in order to guide the agency as it issued a new BiOp. In their Motion for a Stay, Defendants also represented to the Court that they expected to complete the new BiOp within 180 days, placing the date of completion at approximately May 12, 2002. See id. Ex. A, at 3; id. Ex. B ¶ 7 (“NMFS estimates that a new biological opinion will be issued within 180 days.”). Accordingly, Defendants were operating under two deadlines: (1) the good faith representation they made to the Court and (2) the pending expiration of the emergency interim rule regulating the Pelagics FMP, 66 Fed.Reg. 31,561 (June 12, 2001) (extended for an additional 180 days by 66 Fed.Reg. 63,630 (Dec. 10, 2001)), which was due to expire on June 8, 2002. Despite the press of these two deadlines, the new BiOp was not completed within 180 days; in fact, it took NMFS almost 11 months to issue the 2002 BiOp. See 2002 BiOp AR-717, at 6012 (indicating that the 2002 BiOp was not issued until November 15, 2002). After NMFS indicated that it would reinitiate consultations, the United States District Court for the District of Hawaii transferred the Conservation Groups’ suit to this Court. On February 11, 2002, the Conservation Groups’ case — challenging the 2001 BiOp as inadequate to protect the listed turtles — was consolidated with the present action. HLA v. NMFS, Civ. No. 01-0765 (D.D.C. Feb. 11, 2002) (order consolidating this case with Turtle Island Restoration Network v. NMFS, Civ. No. 02-153 (D.D.C.)). On March 19, 2002, the Court issued an order referring Plaintiffs Motion for Partial Summary Judgment — which challenged the 2001 BiOp on procedural grounds — to Magistrate Judge John M. Facciola for a Report and Recommendation pursuant to Local Civil Rule 72.3(a). HLA v. NMFS, Civ. No. 01-0765 (Mar. 19, 2002) (order referring Plaintiff’s Motion for Partial Summary Judgment to Magistrate Judge Facciola). In his April 25, 2002, Report and Recommendation, Magistrate Judge Facciola recommended that HLA’s motion be granted in part and denied in part. HLA v. NMFS, Civ. No. 01-0765, slip op. at 17, 2002 WL 732363 (D.D.C. April 25, 2002) (Report & Recommendation). Magistrate Judge Facciola determined that HLA was an “applicant” under the ESA and NMFS’s implementing regulations, and that HLA had been denied its rights as an “applicant” during the completion of the 2001 BiOp. Id. at 17, 2002 WL 732363. Additionally, Magistrate Judge Facciola found that, as an applicant, Plaintiff should have been provided with a copy of the draft BiOp prior to the agency finalizing it, under the agency’s regulations. Id. at 24, 2002 WL 732363. Magistrate Judge Facciola suggested that fourteen days was a sufficient period of time for Plaintiff to review the draft opinion and provide comments. Id. at 26, 2002 WL 732363. Lastly, Magistrate Judge Faccio-la noted that since the agency was to promulgate a new BiOp by May of 2002, Plaintiffs argument that the BiOp should be remanded to the agency was no longer necessary to consider. Id. at 25-26, 2002 WL 732363. After a joint request for an extension of time, on May 29, 2002, both parties filed objections to Magistrate Judge Facciola’s Report and Recommendation pursuant to Local Civil Rule 72.3(b). Plaintiff stated that it objected to Magistrate Judge Facei-ola’s statement that it was no longer seeking remand of the 2001 BiOp. Pl.’s Limited Objection to Report & Recommendation at 1. In fact, Plaintiff noted that NMFS was now not in a position to issue a new BiOp until mid-November. Id. at 3 n. 3. Given that fact, Plaintiff reiterated its demand that the 2001 BiOp be remanded to the agency. Plaintiff also argued that Magistrate Judge Facciola’s suggestion that the comment period last fourteen days was inadequate to satisfy its needs. Id. at 1. Defendants’ objections essentially tracked their earlier arguments made before Magistrate Judge Facciola, namely that Plaintiff was not an applicant under the agency’s rules, and, even if Plaintiff were an applicant, it was not entitled to a copy of the 2001 BiOp prior to its issuance. Defs.’ Objections to Report & Recommendation at 1. These objections were followed by a volley of responses and replies, which concluded on June 17, 2002. See HLA v. NMFS, Civ. No. 01-0765, slip op. at 4-5 (D.D.C. Sept. 24, 2002). (6) Promulgation of the June 2002 Regulations While the parties were registering their objections to Magistrate Judge Facciola’s Report and Recommendation, NMFS was busy implementing the RPA from the then-valid 2001 BiOp, having obtained West Pac’s approval prior to intimating to the Court that it would issue a new BiOp. Thus, despite Magistrate Judge Facciola’s Report and Recommendation, which determined that the 2001 BiOp was procedurally deficient and the agency’s own decision to issue a new BiOp, NMFS still decided to codify the terms of the 2001 BiOp’s RPA. On April 29, 2002, NMFS published notice in the Federal Registrar of a proposed rule to implement the RPA. 67 Fed.Reg. 20,945 (April 29, 2002) (“NMFS issues this proposed rule that would implement the reasonable and prudent alternatives of the March 29, 2001, Biological Opinion (BiOp) issued by NMFS under the Endangered Species Act (ESA).”). In a letter dated May 18, 2002, HLA submitted comments on the proposed rule. 2002 Regulations AR-219, at 2848. The letter contended that the 2001 BiOp was “unlawfully prepared, substantively flawed, and outdated.” Id. at 2850. On May 20, 2002, West Pac prepared a recommended Regulatory Amendment, including a Regulatory Impact Review and Final Regulatory Flexibility Analysis. 2002 Regulations AR-228, at 2873. In the May 20, 2002, Regulatory Amendment, West Pac considered five alternative actions, including the RPA from the 2001 BiOp as required under the Magnuson-Stevens Act. Id. at 2908. However, West Pac considered these other alternatives, which differed from the RPA, merely “theoretical.” Id. Under the “No Action” alternative, for example, West Pac hypothesized that, had the Council failed to implement the RPA, “NMFS would either implement the reasonable and prudent alternative of the BiOp via a unilateral Secretarial amendment to the FMP’s regulations, or would close one or more FMP fisheries until it reached a decision on how to proceed.” Id. In addition, under the section headed “Measures Taken to Minimize Impacts on Small Businesses,” West Pac noted that the preferred alternative is the only alternative that meets the requirements of the Endangered Species Act, (without closing one or more fisheries) through implementation of the reasonable and prudent alternative contained in the March 29, 2001 Biological Opinion. All other alternatives were either rejected on the grounds that they would either not meet this legal requirement or they would close one or more fisheries. Specifically, Alternatives A, C, D, and E did not meet the legal requirements of the Endangered Species Act Mandated Biological Opinion. Id. at 2924. Moreover, West Pac interjected into this report a theory of transferred effects, noting that “[ujntil other countries adopt similar standards, regulations that remove vessels or landings from western Pacific domestic pelagic fleets may be a relatively ineffective tool [sic] for limiting the global mortality of turtles. The result would likely be to simply transfer the fish harvests (and consequently turtle interactions) to unregulated fisheries.” Id. at 2926. On May 28, 2002, NMFS issued a Record of Decision (ROD), which adopted the FEIS’s Alternative 10 (the RPA) as the preferred alternative. See 2002 Regulations AR-242, at 2979-82. The ROD reiterated that the FEIS’s preferred alternative adopted, by reference, the 2001 BiOp’s RPA. See id. at 2977-78. In addition, the ROD noted that “the final agency decision requires several Western Pacific Fishery Management Council (Council) recommendations and NMFS decisions and actions. The Council process is now complete for measures to implement the agency’s final action. Major Council actions were completed during a meeting held October 23-26, 2001 ....” Id. at 2978 (emphasis added). Finally, in a memorandum accompanying the ROD, NMFS indicated that “[t]hese measures implement the reasonable and prudent alternatives contained in NMFS’ March 29, 2001, Biological Opinion.” Id. at 2969. On June 12, 2002, NMFS issued the now-contested Final Rule. 67 Fed.Reg. 40,-232 (June 12, 2002). The June 2002 Regulations declared, on several occasions, that the rule “implements the reasonable and prudent alternative of the March 29, 2001, Biological Opinion.” Id. at 40,232; id. at 40,233 (same); id. at 40,235 (same); id. (“This final rule implements the non-discretionary reasonable and prudent alternative, as well as non-discretionary terms and conditions also in the BiOp.”) (emphasis added); see also 2002 Regulations AR-242, at 2985 (stating that major components of the adopted alternative “are sea turtle conservation measures, including monitoring, enforcement, and interaction mitigation measures to ensure that continued utilization of sustainable fisheries in the western Pacific region are not likely to jeopardize the continued existence of ESA listed species ”) (emphasis added). In addition, NMFS listed the above-mentioned comments submitted by Plaintiff contending that the BiOp upon which the regulations are based was “unlawfully prepared, substantively flawed, and outdated.” 67 Fed.Reg. 40,232 at 40,234 (June 12, 2002); see also supra note 24. NMFS responded by stating that it believed that the 2001 BiOp “represents the best available science concerning the status of endangered and threatened sea turtles,” but did not address Plaintiffs other criticisms. Id. (7) Plaintiff’s Motion to Amend and the Court’s September 24, 2002, Opinion On July 9, 2002, Plaintiff sought leave from the Court to amend its complaint to add a second claim for relief challenging the June 2002 Regulations, which were premised on the 2001 BiOp. The Court granted the unopposed motion to amend on September 24, 2002. As a result of the Court’s order, Plaintiffs complaint contained two separate counts: one challenging the 2001 BiOp (Count I) and the other challenging the June 2002 Regulations (Count II). Also on September 24, 2002, the Court issued a memorandum opinion and order vacating and remanding the 2001 BiOp. HLA v. NMFS, Civ. No. 01-0765, slip op. at 5 (D.D.C. Sept. 24, 2002). The Court determined that Plaintiff was an “applicant” under NMFS’s own regulations, see 50 C.F.R. § 402.02; 50 C.F.R. § 402.14(g)(5), and should have been afforded time to review and comment on the 2001 BiOp. HLA v. NMFS, Civ. No. 01-0765, slip op. at 5-6 (D.D.C. Sept. 24, 2002). Moreover, as an “applicant,” Plaintiff was entitled to reasonable time to review and comment on the 2002 BiOp before its promulgation. Id. At the same time, the Court delayed issuing its remand order until November 15, 2002, the date that NMFS represented that the 2002 BiOp would finally be released. Id.; see also id. at 9-11. Indeed, the Court was reluctant to remand the 2001 BiOp to the agency and leave no regulations in place until the 2002 BiOp [was] issued, given the concerns expressed by the agency and environmental groups in the case. Thus, until November 15, 2002, the Court [decided to] leave the current regulatory regime in place and use its equitable powers to stay this case until that date. Id. at 11 n. 8. Under the assumption that these actions rendered the second count of Plaintiffs amended complaint (challenging the June 2002 Regulations, which were premised on the 2001 BiOp’s RPA) moot, on November 15, 2002, the Court vacated and remanded the 2001 BiOp and dismissed both counts of Plaintiffs complaint with prejudice. , HLA v. NMFS, Civ. No. 01-0765 (D.D.C. Nov. 15, 2002) (order vacating and remanding the 2001 BiOp to NMFS and dismissing the case with prejudice). In light of the fact that the 2001 BiOp had been vacated, and given that a new BiOp had been issued, the Court also dismissed the Conservation Groups’ suit, which challenged the adequacy of the now-moot 2001 BiOp. Id. (8) The 2002 BiOp As indicated above, on December 17, 2002, Defendants notified the Court of their decision to reinitiate consultations and issue a new BiOp, which would effectively supplant the contested 2001 BiOp. Defs.’ Mot. for Stay at 1; see also supra 18-20. There is some dispute over Defendants’ motivation in reinitiating consultations, particularly given the fact that Defendants’ Opposition was due on the substantive challenge to the 2001 BiOp at the time that they presented their Motion for Partial Dismissal, or in the Alternative, for a Stay. In Plaintiffs Statement of Material Facts, HLA contends that “[t]he ‘new reinitiation strategy’ was intended to ‘circumvent’ judicial review of the 2001 BiOp and generate a more supportive administrative record without any intention of reconsidering the 2001 BiOp jeopardy opinion or RPA.” Pl.’s Statement of Material Facts in Support of Third Claim for Relief (“Pl.’s Statement of Facts, Third Claim”) ¶ 38. In support of this contention, Plaintiff cites several e-mails sent by NMFS personnel: The pressure: the opposition to HLA’s motion for summary judgment is due December 17. Adam [Issenberg, attorney for Defendants,] would like to circumvent that by calling a status conference with the Court next week. That is the opportunity to present our new rein-itiation strategy. 2002 BiOp AR-105, at 798 (Dec. 13, 2001, e-mail from Judson Feder, NMFS Southwest Regional Counsel, to Rod Mclnnis, Acting Regional Administrator). The schedule discussion [provided to the Court] indicates that within the first 30 days we will determine if the original proposal [in the 2001 BiOp] still causes jeopardy. I have not seen or heard of this twist in the discussions thus far. Thus far I have heard that we are not revisiting the original analysis [in the 2001 BiOp] (other than to clarify some points) and the original conclusions stand. 2002 BiOp AR-111, at 810 (Dec. 12, 2001, e-mail from Penny Ruvelas, NMFS Section 7 Regional Coordinator to Judson Feder, NMFS Southwest Regional Counsel) (emphasis added). What we are going to do is very different than reassessing our findings [in the 2001 BiOp]. Craig and I will be working together to better explain/clarify the steps taken in the jeopardy analysis. We may beef up certain discussions and explanations in the Effects of the Action section and revise some language within the species response section to hopefully get the point across better. This is “very different than sitting down with the data again and redoing our jeopardy analysis.” 2002 BiOp AR-113, at 819 (emphasis added). “Defendants dispute [Pjlaintiffs characterization of the administrative record,” but focus exclusively on Plaintiffs aver-ments regarding Defendants’ motivation. Defs.’ Response to Pl.’s Statement of Material Facts with Respect to the Third Claim for Relief (“Defs.’ Response to Pl.’s Statement, Third Claim”) ¶ 38. Because the Court finds Defendants’ motivations immaterial, it will not consider that matter any further. However, whether the 2002 BiOp constituted a reevaluation of the vacated 2001 BiOp is material to the resolution of this action. In this regard, Defendants do not contest Plaintiffs statement that NMFS had no “intention of reconsidering the 2001 BiOp jeopardy opinion or RPA,” nor do they proffer any evidence in the Administrative Record that refutes this statement. See id. Therefore, Defendants have failed to dispute Plaintiffs statement about the scope of the 2002 BiOp and the Court concludes, under Local Civil Rule 56.1, that Defendants had no “intention of reconsidering the 2001 BiOp jeopardy opinion or RPA.” As the Court also indicated above, when NMFS moved for Partial Dismissal, or in the Alternative, for a Stay, it made clear that it had “decided to reinitiate consultation and prepare a new biological opinion.” Defs.’ Mot. for Stay at 2; see also Defs.’ Reply, Mot. for Stay at 2 (stating that “the 2001 BiOp has limited continuing applicability and will soon be superceded”) (emphasis added). Defendants also attached a memorandum from Rodney R. Mclnnis, Acting Regional Director of NMFS, indicating that new information is available which may improve NMFS’ ability to quantify and evaluate the effects of the United States’ pelagic fisheries and the reasonable and prudent alternatives in the BiOp on fist-ed turtle populations. Therefore, ... NMFS is reinitiating section 7 consultation under the Endangered Species Act (ESA) on the potential effects of the pelagic fisheries under the FMP on threatened and endangered species. Id. Ex. A, at 1 (emphasis added) (also available at 2002 BiOp AR-114, at 821). The letter went on to note that “observer data since 1999 is available which may affect the estimated direct and indirect effects of the fisheries and the expected results of the reasonable and prudent alternative.” Id. Despite these representations to the Court, by mid-December, 2001, the e-mails cited by Plaintiff — and not disputed by Defendant (as they relate to the scope of the 2002 BiOp) — make clear that NMFS was doing something “very different than reassessing [its] findings” in the 2001 BiOp.2002 BiOp AR-113, at 819 (“This is very different than sitting down with the data again and redoing our jeopardy analysis.”). Indeed, almost ten months later, “on October 9, 2002, NMFS announced ... that the scope of the ‘action’ under consideration had changed from the Fishery as operated prior to the 2001 BiOp to the ‘fisheries as they operate today,’ meaning the Fishery after NMFS implemented the RPA of the 2001 BiOp.” Pl.’s Statement of Facts, Third Claim ¶ 49 (citing 2002 BiOp AR-464, at 4070-87). Specifically, a memorandum issued by Dr. Charles Kar-nella, Administrator for the Pacific Islands Area Office (“PIAO,” or the “action” component NMFS) indicated that PIAO requested that the ongoing consultation be amended: The PIAO requests the Office of Protected Resources (consulting agency) ... amend the ongoing consultation to include evaluation of the pelagic fisheries under the [Pelagies FMP] as they now operate. By this we mean the fisheries regulated under the [Pelagies FMP] subsequent to issuance by NOAA Fisheries of the Biological Opinion on Authorization of Pelagic Fisheries under the [Pelagies FMP] (BiOp) on March 29, 2001, and as described by the preferred alternative contained in the [Pelagies FMP] Final Environmental Impact Statement (FEIS) issued by NOAA Fisheries on March 30, 2001. The “proposed action” would be the fisheries as they operate today. 2002 BiOp AR-464, at 4070 (memorandum dated Oct. 9, 2002) (emphasis added). Plaintiff asserts in its Statement of Material Facts that “[t]he record is devoid of any explanation for NMFS’ decision to change the scope of consultation.” Pl.’s Statement of Facts, Third Claim ¶ 50. Defendants respond by noting, among other things, (1) that after NMFS’s December 2001 decision to reinitiate, there was some “confusion” over the scope of the re-consultation, Defs.’ Response to Pl.’s Statement, Third Claim ¶ 50; (2) that Dr. Karnella (author of the October 9, 2002, memorandum amending the scope of the 2002 BiOp) “had stated as early as April [2001] that ‘given the passage of time and unfolding of events’ consulting on the fisheries as they existed prior to the date of the CMC injunction ‘comes across as artificial and contrived,’ ” id. (citing 2002 BiOp AR-233, at 2004); and (3) that “much of the newer data used in consultation related to the present fishery, not to the pre-1999 fishery, and therefore a disconnect resulted,” id. (citing 2002 BiOp AR-233, at 2004-05, 2007). While Defendants’ response may offer a reasoned explanation as to why NMFS decided to change the scope of the 2002 BiOp, it does not offer any explanation as to how the amended scope of the 2002 BiOp remained consistent with the representations Defendants made to the Court on December 17, 2001, nor does it offer any explanation as to the legality of the 2002 BiOp, particularly given the fact that it did not revisit the conclusions of the vacated, and procedurally deficient, 2001 BiOp. Furthermore, it is undisputed that, at least until the spring of 2002, “NMFS prepared a draft opinion based on the fishery as it was operating in 1999.” Defs.’ Response to Pl.’s Statement, Third Claim ¶ 51; see also Pl.’s Statement of Facts, Third Claim ¶ 51. Nonetheless, it is also apparent from the Record that — by at least October 9, 2002 — NMFS decided to change course. 2002 BiOp AR-464, at 4070. In the interim, NMFS failed to meet the good-faith May 2002 deadline it provided to the Court, see Defs.’ Mot. for Stay, Ex. A, at 3; id. Ex. B ¶ 7 (“NMFS estimates that a new biological opinion will be issued within 180 days.”), and the expiration of the emergency interim rule, see 66 Fed.Reg. 63,630 (Dec. 10, 2001) (expiring June 8, 2002). After NMFS formally amended the scope of the 2002 BiOp, however, it was able to render its final decision in slightly more than a month. See 2002 BiOp AR-464, at 4070 (memorandum amending the scope of the 2002 BiOp, dated October 9, 2002); 2002 BiOp AR-717, at 6012 (November 15, 2002, BiOp). On November 15, 2002, NMFS released the 2002 BiOp. Id. The scope of the 2002 BiOp was entirely consistent with the October 9, 2002, memorandum: “the management regime, as modified by adoption of the Reasonable and Prudent Alternative in the March 2001 Biological Opinion and described by the preferred alternative of the March 2001 FEIS by NMFS ... constitute the action being considered in this opinion.” Id. at 6018. Thus, as its baseline, the 2002 BiOp relies on the conclusions of the vacated and remanded 2001 BiOp, and does not constitute a reexamination of the 2001 BiOp’s conclusions. Based on its “as regulated” baseline, the 2001 BiOp reached a “no jeopardy” conclusion. See id. at 6012, 6267-68. Just as important, NMFS did not promulgate new regulations to supplant those codified on June 12, 2002 (the contested June 2002 Regulations). As a practical result of the 2002 BiOp’s “no jeopardy” conclusion, NMFS was not required to initiate a new set of RPAs. More importantly from Plaintiffs perspective, NMFS was not required to consult with HLA as an “applicant” — at least, regarding the issue of a new set of RPAs— because NMFS was not required to develop any RPAs under its “no jeopardy” finding. Instead, the 2002 BiOp issued a revised series of Incident Take Statement levels. Id. at 6328-30. The net result of the agency’s behavior was that NMFS effectively insulated the substance of the 2001 BiOp from Court review. (9) Plaintiff’s Motion for Reconsideration and Related Matters On November 25, 2002, Plaintiff timely filed a Combined Motion for Reconsideration, for an Expedited Hearing, and for Leave to File an Amended Complaint and Take Discovery. Because the Court was compelled to consider a motion for reconsideration under Federal Rules of Civil Procedure 59(e) or 60(b) prior to granting leave to amend, see Firestone v. Firestone, 76 F.3d 1205, 1208 (D.C.Cir.1996), the Court entertained Plaintiffs motion to reconsider separately. As a result, on January 17, 2003, the Court first issued a Memorandum and Order regarding Plaintiffs motion to reconsider. HLA v. NMFS, Civ. No. 01-0765 (D.D.C. Jan. 17, 2003) (memorandum and order granting in part and denying in part Plaintiffs motion for reconsideration). In granting in part Plaintiffs unopposed motion to reconsider under Rule 59(e), the Court observed: Although the June 12, 2002, regulations were already in force when the Court issued its November 15, 2002, order, the Court was under the impression that by vacating the 2001 BiOp, the regulations on which it was premised would also fall. Nonetheless, the parties do not dispute the fact that the regulations are still in force, and the Plaintiff was never granted a hearing on the second count of its amended complaint, challenging these regulations. Id. at 4. Thus, “in order to avoid manifest injustice,” the Court granted Plaintiffs unopposed motion to reconsider the second count of its complaint, but — having already vacated the 2001 BiOp — denied Plaintiffs motion with respect to the first count of its complaint. Id. After dispensing with Plaintiffs motion to reconsider, the Court issued a separate Memorandum and Order regarding Plaintiffs motions to amend its reinstated complaint, for an expedited hearing schedule, and to take discovery. HLA v. NMFS, Civ. No. 01-0765, slip op. at 1 (D.D.C. Jan. 17, 2003) (memorandum and order). The Court granted Plaintiffs motion to amend pursuant to Federal Rule of Civil Procedure 15(d), observing that Plaintiffs supplemental pleading was “so intertwined in the proceedings already before the Court” that it justified granting Plaintiff leave to amend. Id. at 7. The Court also granted Plaintiffs motion for an expedited hearing schedule, observing that the Magnuson-Stevens Act provides for expedited consideration of Plaintiffs second claim. Id. (citing 16 U.S.C. § 1855(f)(4)). Finally, the Court denied, without prejudice, Plaintiffs motion to take discovery related to the third count of its reinstated, amended complaint, challenging the 2002 BiOp. Id. at 8-9. (10) The Conservation Groups’ Second Motion to Intervene After the Court reopened Plaintiffs case, the Conservation Groups again filed a motion to intervene — this time in order to defend the June 2002 Regulations and the 2002 BiOp. On August 31, 2003, the Court granted the Conservation Groups’ motion, but expressly limited the scope of intervention to defending NMFS’s actions. (11) The Present Cross-Motions for Partial Summary Judgment After the Court reopened this case and readmitted Defendant-Intervenors, and Defendants submitted the remaining portions of the Administrative Record, this protracted litigation was once again ripe for disposition. Pursuant to the briefing schedule established in the Court’s January 17, 2003, Orders, the parties presented their Cross-Motions for Summary Judgment regarding Plaintiffs second claim for relief, challenging the June 2002 Regulations, and Plaintiffs third claim, seeking to overturn the 2002 BiOp. Plaintiffs reinstated, Second Amended Complaint alleges that the June 2002 Regulations were promulgated in violation of the Administrative Procedure Act (“APA”), 5 U.S.C. § 701, et seq.-namely, that the Rule “was not completed in accordance with law, is arbitrary and capricious, and an abuse of discretion.” Sec. Am. Compl. ¶ 62. For the same legal reasons, Plaintiff also challenges the 2002 BiOp. Id. ¶ 66. Consequently, Plaintiff requests, among other things, that the Court remand the 2002 BiOp to NMFS for preparation of a new BiOp; set aside the June 2002 Regulations; enjoin NMFS to prepare the new BiOp through a lawful process that provides Plaintiff, and West Pac, a meaningful opportunity to review and comment on the new BiOp as “applicants”; enjoin NMFS to prepare the new BiOp pursuant to a court-approved schedule; enjoin NMFS to adopt a court-approved interim Fishery management regime pending the completion of the new BiOp; and award Plaintiff its reasonable fees, costs, expenses, and disbursements associated with this litigation. Id. at 21 (“Wherefore” Paragraph). II. LEGAL STANDARD The APA empowers the Court to “hold unlawful and set aside agency action, findings, and conclusions found to be ... arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law,” “in excess of statutory jurisdiction, authority, or limitations, or short of statutory right,” or “without observance of procedure required by law.” 5 U.S.C. § 706(2)(A), (C) and (D). Although the judiciary bears the responsibility under the APA to set aside agency decisions that meet this description, see MD Pharmaceutical, Inc. v. Drug Enforcement Admin., 133 F.3d 8, 16 (D.C.Cir.1998); Utility Solid Waste Activities Group v. EPA, 236 F.3d 749, 755 (D.C.Cir.2001), “[t]he scope of review under the ‘arbitrary and capricious standard’ is narrow and a court is not to substitute its judgment for that of the agency.” Motor Vehicle Mfrs. Ass’n v. State Farm Mut. Auto. Ins. Co., 463 U.S. 29, 43, 103 S.Ct. 2856, 77 L.Ed.2d 443 (1983). Nonetheless, this Circuit has held that “where the agency has failed to provide a reasoned explanation, or where the record belies the agency’s conclusion, we must undo its action.” Petroleum Communications, Inc. v. FCC, 22 F.3d 1164, 1172 (D.C.Cir.1994) (citing American Tel. & Tel. Co. v. FCC, 974 F.2d 1351, 1354 (D.C.Cir.1992)). Summary judgment is appropriate if the record, viewed in the light most favorable to the nonmoving party, reveals that there is no genuine issue of material fact and the moving party is entitled to judgment as a matter of law. See Tao v. Freeh, 27 F.3d 635, 638 (D.C.Cir.1994); Fed.R.Civ.P. 56(c); see also Celotex Corp. v. Catrett, 477 U.S. 317, 322, 106 S.Ct. 2548, 91 L.Ed.2d 265, (1986). Similarly, in ruling on cross-motions for summary judgment, the court shall grant summary judgment only if one of the moving parties is entitled to judgment as a matter of law upon material facts that are not genuinely disputed. See Rhoads v. McFerran, 517 F.2d 66, 67 (2d Cir.1975); Long v. Gaines, 167 F.Supp.2d 75, 85 (D.D.C.2001). Summary ju