Royce C. Lamberth, Chief Judge
Defendants object to the report and recommendation (“R&R”) of Magistrate Judge Facciola, ECF No. 49, recommending that this Court deny the cross-motions for summary judgment pendente lite and remand the case. ECF No. 56. Because the defendant agency has taken actions which render this case moot, the Court overrules the R&R and dismisses the case.
A. The Regulatory Regime
The National Marine Fisheries Service (“NMFS” or “the Service”)—part of the National Oceanic and Atmospheric Administration, and, in turn, the Department of Commerce—regulates United States fisheries. See Magnuson-Stevens Fishery Conservation & Management Act (“MSA”), 16 U.S.C. §§ 1801 et seq. NMFS discharges its responsibilities through subsidiaries known as “regional fishery management councils, ” such as the New England Fishery Management Council (“NEFMC” or “the Council”). § 1852(a)(1)(A). Each regional council is “required to implement congressional policies in its region by developing a fishery management plan (‘FMP’), as well as necessary amendments thereto.” Fishing Co. of Alaska, Inc. v. Gutierrez, 510 F.3d 328, 330 (D.C. Cir. 2007) (citing § 1852(h)(1)). Each council must also “propose regulations to implement the FMP” to the Secretary of Commerce, who “must then review the proposed regulations” and either “return the regulations to the Council with proposed revisions” or “publish the regulations for comment in the Federal Register” and, after notice and comment, must ultimately “promulgate final regulations.” Id. (citing §§ 1853(c), 1854(b)(1)(A)– (B), (b)(3)). The Secretary is “bound by the judicial review provisions of the Administrative Procedure Act including the requirement that his actions not be ‘arbitrary, capricious, an abuse of discretion, or otherwise not in accordance with law.’” Id. (citing § 1855(f); 5 U.S.C. § 706(2)(A)).
B. Regulatory History
Congress has embraced the goal of minimizing, to the extent practicable, quantities of “bycatch”—fish caught by fisherman attempting to catch other species which are not kept but are nevertheless dead or dying when returned to the ocean. See Fishing Co., 519 F.3d at 330 (citing 16 U.S.C. § 1801(c)(3)); see also 16 U.S.C. § 1851(a)(9) (“Conservation and management measures shall, to the extent practicable, (A) minimize bycatch and (B) to the extent bycatch cannot be avoided, minimize the mortality of such bycatch.”); R&R 2 & n.1. This case is about protecting New England (NE) multispecies fish (“groundfish”) against bycatch-induced overfishing. R&R 3.
In the early 1990s, excessive groundfish bycatch led the Service, at the Council’s request, to close areas in the New England fishery to any fishing gear capable of catching groundfish. See Fishery Conservation & Management: Northeast Multispecies, 59 Fed. Reg. 63, 926 (Dec. 12, 1994), amended 60 Fed. Reg. 3, 102 (Jan. 13, 1995); see also NE Multispecies Fishery, Amendment 7, 61 Fed. Reg. 27, 710–50 (May 31, 1996) (continuing and expanding closures). In the following decade, the Service—again, at the Council’s request—relaxed this ban. In 1998 the Service implemented Framework Adjustment 18, allowing herring and mackerel fishers employing mid-water trawl gear to fish in the previously closed areas subject to a one-percent groundfish bycatch limit and other conditions. See Framework Adjustment 18, 63 Fed. Reg. 7, 727 (Feb. 17, 1998), 50 C.F.R. Part 648. And in 2006 the Service implemented Framework Adjustment 43 which further modified the bycatch restrictions on herring fishers by setting a 0.2-percent haddock catch cap, establishing an exempted herring fishery, and making other changes. Framework Adjustment 43, 71 Fed. Reg. 46, 871 (Aug. 15, 2006), 50 C.F.R. Part 648.
C. Plaintiffs’ Petition
In 2007, plaintiffs petitioned the Secretary of Commerce seeking emergency and permanent rulemaking, pursuant to 16 U.S.C. § 1855(c) and (d), to exclude midwater trawl vessels from closed areas. Petition for Immediate and Permanent Rulemaking to Protect Groundfish from Midwater Trawl Fishing in Northeastern Groundfish Closed Areas (“Petition”), Oct. 12, 2007, ECF No. 1-1. The petition musters evidence purporting to demonstrate that bycatch levels by these vessels are exceeding the limits set by Framework Adjustments 18 and 43, Petition 10–13, and that the agency’s data-collection system is unreliable because it systematically underreports bycatch, Petition 13–17.
D. NMFS’ Rejection
The Service promptly rejected the petition. Regional Administrator Patricia Kurkul reviewed it, and transmitted a memoranda to William Hogarth, Assistant Administrator for Fisheries, recommending denial on the grounds that there “have been no indications that [the catch-cap imposed by Framework Adjustment 43] has been caught” and “Petitioners provide no significant new information to justify emergency action at this time.” Administrative Record(“AR”) 911–12; see also R&R 13. Mr. Hogarth sent a letter to petitioners denying their petition, noting that NEFMC had “considered prohibiting midwater trawls in these closed areas before, and has determined that the bycatch of NE multispecies was not sufficient to justify this action, ” and that “observer data available continue to suggest that bycatch levels are within the range considered acceptable by the Council.” AR 915. Further, the letter explained that the petition did “not contain significant new information that demonstrates an emergency in the fishery.” Id.
E. Judge Facciola’s Report and Recommendation
Plaintiffs filed suit and, in 2010, ruling on cross-motions for summary judgment, Magistrate Judge Facciola found that the Service’s rejection may have been arbitrary and capricious in violation of the APA. R&R 22. “[T]he petitioners and the agency passed like ships in the night, ” he concluded, because “the agency relied on the very data called into question by plaintiffs for its decision to deny the Petition, without any explanation as to why it found the data sufficient and worthy of reliance.” R&R 19, 22. Judge Facciola recommended that the cross-motions for summary judgment be denied pendente lite while the matter was remanded to the Service to explain “why it rejected the assertion by ...