1 UNITED STATES DISTRICT COURT FOR THE DISTRICT OF COLUMBIA

__________________________________ ) AIR TRANSPORT ASSOCIATION ) OF AMERICA, INC. d/b/a ) AIRLINES FOR AMERICA, et al. , ) ) Plaintiffs, ) ) v. ) ) Civil Action N o. 16-919 (RMC) UNITED STATES DEPARTMENT ) OF AGRICULTURE, et al. , ) ) Defendants. )

_________________________________ )
OPINION The Agriculture Quarantine Ins pection program is an essential p art of the nation’s efforts to secure its plants a nd animals from pests and disease s that are not native to the territory of the United States. The Anima l and Plant Health Inspection S ervice (APHIS), an agency within the Department of Agricul ture, works with Customs and Bo rder Protection (CBP), an agency within the Department of Homeland Security (DHS), to ins pect all persons and vessels entering the United States. I n 1990, Congress ordered APHIS to charge its costs for the required inspections to the applicable c lasses of users; since then, APH IS has proposed various rules concerning fees for different us er classes. In 2015, APHIS ado pted a rule which set a new fee structure. Under that rule, int ernational airline passengers a re charged a Passenger Fee of $3.96 (reduced from $5) and international commercial aircraft are cha rged a Commercial Aircraft Fee of $225 (increased from $70.75). The Air Transport Associationof America, Inc. and the International Air Transport A ssociation (coll ectively, Plaintif fs) challenge the validity of the rule. They argue that it is inc onsistent with the governing st atutory provisions and violates the Administrative Procedur e Act (APA), 5 U.S.C. § 500 et seq. (2012).2 Having studied the parties’ brie fs, oral arguments, and the ent ire record, the Court finds that (1) Plainti ffs’ claims are not time-barred; (2) APHI S’s actions were consistent with the governing statute in charging both a n air passenger fee and commercial aircraft fee to passenger aircraft; (3) APHIS has not unlaw fully engaged in cross-subsidi zation; (4) APHIS and Grant Thornton, LLP reasonably relied on the fiscal year (FY) 2010 an d 2011 data; and (5) Plaintiffs were not harmed by the withholding of some data during the noti ce and comment period. The Court also finds t hat after FY02, the gove rning statute no long er permitted APHIS to set fees in order to maintain a reasonable ba lance, which APHIS used to fun d its reserve account. Thus, the Court will deny Defendants’ motion to dismiss, grant summary ju dgment to Defendants on Counts I, II, and IV, and grant summary judgment in favor of Pl aintiffs on Count III and remand this part of the rulemaking for further consideration and possi ble rulemaking by APHIS.
I. BACKGROUND APHIS has been inspecting “pers ons and vessels entering the cus toms territory of the United States for possible infection or inf estation with pe sts and diseases that threaten the resident flora and fauna” of the United States for over a centu ry. Defs.’ Mem. of P. & A. in Supp. of Their Mot. to Dismiss and for Summ. J. and in Opp’n to Pls.’ Mot. for Summ. J. (APHIS Opp’n) [Dkt. 24-1] at 1; see also Plant Protection Act, 7 U.S.C. § 7701 et seq . (2010); 7 C.F.R. § 330.105. The inspections are conducted through the Ag ricultural Quara ntine Inspection (AQI) program. Prior to the e nactment of the Food, Agriculture , Conservation, and Trade (FACT) Act of 1990, Pub. L. No. 101-624, § 2509, 104 Stat. 3359 , 4069-70 (1990) (current version at 21 U.S.C. § 136a (2013)), the costs of AQI were cove red by annual appropriations to the Department of Agriculture.3 However, in 1990, Congress enacted th e FACT Act, which “authori zes [APHIS] to collect user fees f or certain agricultural quarantine and in spection (AQI) servi ces.” Final Rule
at AR229. 1 Because the terms of the statute have changed over time, and are integral to the current dispute, the Court detail s the legislative history. As originally enacted, the FACT Act provided that The Secretary of Agriculture . . . may prescribe and collect fe es to cover the cost of providing agri cultural quarantine and inspect ion services in connection with the arrival at a port in the custom s territory of the United States, or the preclearance or preinspe ction at a site outside the customs terr itory of the United States, of a commercial vessel, commercial aircraft, commercial truck, or railroad car. § 2509(a)(1). The FACT Act was first amended in 1990 to add “i nternational passengers” as a class of persons responsible for paying an AQI fee. See Omnibus Budget Reconciliation Act of 1990, Pub. L. No. 101-508, § 1203, 104 Stat. 1388, 1388-11 (199 0). The original FACT Act required the Secretary to se t and adjust the fees: to reflect the cost to the Secret ary in administering such subs ection, in carrying out the activities at ports in customs territory of the United States and preclearance a nd preinspection sites outside the customs territory of the United States in connection with the provision of agricultural quaran tine inspection services, and i n maintaining a reasonable balance in the Account. § 2509(a)(4). Congress further amended the F ACT Act in 1991. As relevant, the 1991 amendment specified that inspec tion fees may only be collected in an amount commensurate with the costs of inspection f or each class of persons or entit ies paying the fees. See Food,

1 The Administrative Record is located on the Electronic Case Fi ling (ECF) system at docket numbers 30 and 31.4 Agriculture, Conservation, and T rade Act Amendments of 1991, Pu b. L. No. 102-237, § 1015, 105 Stat 1818, 1902 (1991). Fees, including fees from inte rnational airline passengers and commercial aircraft operators, may only be collected to the ext ent that the Secretary reasonably e stimates that the amount of the fees are commensurate with the costs of agricultural quarantine and inspection services with respect to the class of persons or ent ities paying the fees. The costs of such services with respect to passengers as a class in cludes the costs of related inspections of the aircraft. Id . § 1015(a)(1)(D) (emphasis added). The meaning of the highlig hted sentence is strongly disputed here. In response, APH IS set initial fees in 1991 and1992; for international air passengers the fee was $2.00 and for c ommercial aircraft the fe e was $76.75. See 56 Fed. Reg. 14837, 14845 (April 12, 1991) (setting $2 i nternational air pas senger fee); 57 Fed. Reg. 755, 769 (Jan. 9, 1992) (setting $76.75 com mercial aircraft fee).
A. 1996 Amendment The FACT Act was amended again a s part of the Federal Agriculture Improvement and Reform Act of 1996. See Pub. L. No. 104-127, § 917, 110 Stat. 888, 1187-88 (1996) (codified at 21 U.S.C. § 136a (2013)). That amendment c reated a temporary Agricultural Quarantine Inspection User Fee Ac count in the Department of the Treasury where, for FY96 through FY02, “all of the fees c ollected under this subsection and late payment penalties and interest charges collected” as part of AQI were held. 21 U.S.C . § 136a(a)(5)(A) (1996). After FY02, the balance in the Treasury account was to be “credited t o the Department of Agriculture accounts that incur the costs a ssociated with the provision of agricultural qua rantine and inspection services and the adm inistration of this subsection.” Id . § 136a(a)(6). In addition to5 creating a temporary account t o hold AQI fees, the 1996 amendme nt revised the section describing the authorized fees. (1) Fees authorized The Secretary of Agriculture may prescribe and collect fees sufficient— (A) to cover the cost of providing agricultural quarantine and inspection services in connection with the arrival at a port in the customs territory of the United States, or the preclearance or preinspection at a site outside the customs territory of the Un ited States, of an international passenger, commercial vessel, commercial aircraft, commerc ial truck, or railroad car; (B) to cover the cost of administering this subsection ; and (C) through fiscal year 2002, to ma intain a reasonable balance in the Agricultural Quarantine Inspection User Fee Account established under paragraph (5)

. Id . § 136a(a) (emphasis added). As before, the meaning and relev ance of the emphasized sentences are hotly contested.
B. Regulatory History From the time it set the fi rst inspection fees in 1991, APHIS h as indicated that the costs covered by the AQI fee were intended to include “the tota l cost of delivery costs, program support costs, and agency-level support costs, as well as fundi ng the reserve.” APHIS Opp’n at 8 (citing 56 Fed. Reg. 8148, 8151 (Feb. 27, 1991)). Described as a “reasonable balance,” the reserve was designed to cover th ree months’ average operating c osts for the AQI program, see 1992 Interim Rule at AR71769, and was necessary because fees we re (and are) remitted in arrears and the agency needed t o be prepared to handle emergenc ies or unexpected volumes. See 56 Fed. Reg. at 8151. As APHIS explained most recently: The reserve fund ensures that AQI program operations can continue without interruption when service volumes fluctuate due to economic conditions or other circumstances and CBP and APHIS6 are able to adjust their activity to account for the changed ec onomic conditions. Proposed Rule at AR18. Until this litigation, no user has chal lenged funding the reserve. Between FY92 and FY96, the overall c ost of the AQI program wentfrom $85,922,000 to a projected $127,027,001. See 62 Fed. Reg. 3823, 3823 (Jan. 27, 1997). At that point, APHIS recognized that the requirements of notice-and-com ment rulemaking to reset fees was causing user fees to “lag behi nd the level of current costs .” Id . at 3824. In response, APHIS set a schedule of increas ing fees for FY97 through FY 2002. See 62 Fed. Reg. 39747, 39747-48, 39754 (July 24, 1997). This effort was not fully successful an d APHIS further amended the fee schedule in 1999 to cover increasing costs. See 64 Fed. Reg. 43103, 43103 (Aug. 9, 1999). The attack of September 11, 2001 on t he World Trade Center in N ew York City caused a major decline in international passeng er and cargo tra ffic into the United States. Another result of the attack was increased security concerns th at required increased inspections.
See 69 Fed. Reg. 71660, 71660-61 (Dec. 9, 2004). As part of the r esponse to September 11, Congress passed the Homeland S ecurity Act of 2002, which “trans ferred AQI inspections from the U.S. Department of Agriculture (USDA) to the Department of Homeland Security (DHS) and left certain other AQI respons ibilities at USDA.” May 2006 GAO Rep. at AR69965. Thereafter, and continuing to the present, CBP conducts all port-of-entry i nspections (sea, l and, and air) and APHIS provides scientific guidan ce, training, pest identificati on, risk analysis, and other related services. See id . at AR69965 (“In March 2003, more than 1, 800 agriculture specialist s within USDA’s Animal and Plant Health I nspection Service (APHIS) becam e DHS Customs and Border Protection (CBP) employ ees, while USDA retained responsi bility for AQI activities such as setting inspection policy, prov iding training, and collectin g user fees.”). AQI fees collected by APHIS are now shared with CBP t o cover the cost s of that age ncy’s services. In addition,7 CBP receives annual appropriated funds to cover the costs of in spection services where a fee is not collected. See Final Rule at AR253. APHIS i ssued an interim rule in 2004, ra ising fees to address the increased costs t hat followed after September 11. See May 2006 GAO Rep. at
AR69998. The number of international pa ssengers and goods has again incr eased since 2004, although there was a slight downt urn associated with the 2008 r ecession. See AQI Q&A at AR116; Stakeholder Webinar Tr. at AR171. During this period, A PHIS has experienced significant fee shortf alls. Stakeholder Webinar Tr. at AR172, 177.
C. GAO and OIG Investigations The AQI program has been the sub ject of numerous Government Acc ountability Office (GAO) and DHS Office of Ins pector General (OIG) investig ations and studies since CBP became primarily responsible for conducting the inspections in 2003. GAO focused on monitoring the success of the tra nsition from a purely APHIS-ru n program to the combined APHIS/CBP program. GAO first i ssued a report in May 2006, find ing that CBP was understaffed, failed to develop an a dequate way to evaluate per formance, and lacked sufficient data on the cost of the AQI progr am to determine appropriate AQ I fees. See May 2006 GAO Rep. at AR69965, 69970-73, 69999. A February 2007 OIG audit fu rther identified issues with CBP data systems, which resulted in incomplete data and an inab ility to set AQI fees accurately.
See Feb. 2007 OIG Rep. at AR70744-48. In September 2007, a GAO re port addressed the challenges faced by CBP in adminis tering three separate interna tional air passenger inspections, which are funded by three separate statutes. See Sept. 2007 GAO Rep. at AR70039 (explaining that CBP is responsible for cus toms, immigration, and agricultural inspections of incoming international passengers). A February 2008 GAO study again fou nd that CBP lacked sufficient data to track the actual cost of each type of inspection for ea ch type of user class. See Feb. 20088 GAO Rep. at AR70129-30. In September 2012, the GAO conducted f urther review and again found significant data reliabili ty issues and inherent data lim itations associated with the AQI
program. See Sept. 2012 GAO Rep. at AR70267-68, 70277-80. Finally, in Marc h 2013, GAO noted a significant difference between costs and fees collectedand recommended increasing AQI fees. See March 2013 GAO Rep. at AR70568, 70579-84.
D. Current Rulemaking Despite repeated attempts to adjus t fees, as of the rulemaking in 2014-2015 APHIS was still not recovering e nough fees to cover the costs o f AQI inspections. The AQI fees have not been adjusted since FY 2010 and do not reflect the current cost of provi ding AQI services. As a resul t, U.S. Customs and Border Protection (CBP) of the Department of Homeland Security, which collaborates with APHIS in providing . . . AQI services . . . , has relied more heavily on its appropriated funds to provide AQI services that are not paid fo r by AQI revenue or to cover the cost of services for which the curr ent fee revenue is insufficient. Final Rule at AR230. This time, A PHIS retained Grant Thornton LLP, an international audit, tax, and advisory firm, to develop amodel that calculated the appropriate fee for each user class based on the actual costs associat ed with inspecting that user class. Grant Thornton used an “activity-based costing (ABC) met hodology” to determine the app ropriate fee for each user class based on the specific costs that w ere attributed to inspections for that class. May 2012 Grant Thornton Rep. at AR636. The accoun tants first assigned all ass ociated AQI costs to a specific activity and then matched each a ctivity to a corresponding clas s of persons or entities. March 2012 Grant Thornton Rep. at AR442. D espite flaws in the data, Grant Thornton used what was available from FY10 and FY 11 to conduct its analysis. APHIS submitted a proposed new rule for notice and comment on April 25, 2014. Hundreds of comments were received over the next 90 days, see Final Rule at AR230, and9 APHIS issued the Final Rule (F inal Rule or Rule) on October 29, 2015, which decreased the air passenger fee to $3.96 (from $5) and i ncreased the commercial a ircraft fee to $225 (from $70.75). See Final Rule at AR229-60. The relat ed regulation has long define d “commercial aircraft” as “[a]ny aircraft us ed to transport persons or prope rty for compensation or hire.” 7 C.F.R. § 354.3(a). Plaintiffs submitted comments objecting to the proposed rule an d questioning “the application of the commercial ai rcraft fee to passenger aircraf t, the rounding up of fees to fund the AQI reserve, and the nature and quality of the information published in the rulemaking docket.” APHIS Opp’n at 16 (citing Comments of Airlines for Am erica at AR71133-49). After the Rule was published, on May 13, 2016, Plaintiffs filed suit. The Complaint advances four alleged violations of the APA: Count I: The Rule violates the FACT Act’s prohibition against duplicative commercial aircraft fees; Count II: The Rule violates the FACT Act’s prohibition on cros ssubsidization of fees among user classes; Count III: The Rule maintains a reserve, in violation of the F ACT Act removal of APHIS’s authority t o maintain a reserve after 20 02; and Count IV: The Rule was adopted without reasoned decision-makin g due to unreliable data and da ta which was withheld from commenters. Compl. [Dkt. 1] at 36, 37, 39, 40. Def endants answered on July 18, 2016. See Answer [Dkt. 15]. Plaintiffs moved for summary judgment on all claims on March 15, 2017. See Mem. of Law in Supp. of Pls.’ Mot. for Sum m. J. [Dkt. 20-1] (Pls.’ Mot. ). Defendants opposed and filed a combined cross motion for summary judgment and motion to dism iss Counts I and III as time barred on May 8, 2017. APHIS Opp’n. P laintiffs filed a consol idated reply and opposition on June 29, 2017, see Pls.’ Consol. Opp’n to Defs.’ Cro ss-Mot. for Summ. J. and Repl y Br. in Supp.10 of Pls.’ Mot. for Summ. J. [Dk t. 26] (Pls.’ Opp’n), and Defenda nts replied. See Defs.’ Reply Mem. in Supp. of Their Mot. to Dis miss and for Summ. J. [Dkt. 2 8] (APHIS Reply). The Court conducted oral argument on March 13, 2018. The motions are rip e for review.
II. LEGAL STANDARD
A. Motion to Dismiss – Sta tute of Limitations An affirmative defense that cla ims are barred by a statute of l imitations may be asserted in a Rule 12(b)(6) moti on “when the facts that give ri se to the defense are clear from the face of the complaint.” Smith-Haynie v. District of Columbia, 155 F.3d 575, 578 (D.C. Cir. 1998). A court may only rule on a sta tute of limitations defen se under Rule 12(b)(6) when the face of the complaint conclusiv ely shows that it is time-barred

. See Performance Contracting, Inc. v. Rapid Response Constr., Inc., 267 F.R.D. 422, 425 (D.D.C. 2010) (citing Smith-Haynie, 155 F.3d at 578); see also Lewis v. Bayh, 577 F. Supp. 2d 47, 51 (D.D.C. 2008); Turner v. AfroAmerican Newspaper Co., 572 F. Supp. 2d 71, 72 (D.D.C. 2008).
B. Motion for Summary Judg ment – Fed. R. Civ. P. 56 Under Rule 56 of the Federal Rules of Civil Procedure, summary judgment shall be granted “if the movant shows that there is no genuine disput e as to any material fact and the movant is entitled to judgment as a matter of law.” Fed. R. Ci v. P. 56(a); accord Anderson v. Liberty Lobby, Inc. , 477 U.S. 242, 247 (1986). “In a case involving review of a f inal agency action under the Administrative Pr ocedure Act, however, the sta ndard set forth in Rule 56[ ] does not apply because of the limited rol e of a court in reviewing t he administrative record.” Sierra
Club v. Mainella , 459 F. Supp. 2d 76, 89 (D.D.C. 2006) (internal citation omitt ed), appeal
dismissed , Nos. 06-5419 & 07-5004, 2007 WL 11 25716 (D.C. Cir. Mar. 30, 2 007); see also Charter Operators of Alaska v. Blank , 844 F. Supp. 2d 122, 126-27 (D.D.C. 2012); Buckingham
v. Mabus , 772 F. Supp. 2d 295, 300 (D.D.C. 2011). Under the APA, the a gency’s role is to11 resolve factual issues to reach a decision supported by the adm inistrative record, while “‘the function of the district court is to determine whether or not a s a matter of law the evidence in the administrative record permitted the agency to make the decision it did.’” Sierra Club , 459 F. Supp. 2d at 90 (quoting Occidental Eng’g Co. v. INS , 753 F.2d 766, 769-70 (9th Cir. 1985)). “Summary judgment thus serves as the mechanism for deciding, as a matter of law, whether the agency action is supported by the a dministrative record and oth erwise consistent with the APA standard of review.” Id. (citing Richards v. INS , 554 F.2d 1173, 1177 & n.28 (D.C. Cir. 1977)).
C. Administrative Procedure Act The APA, requires courts to review agency actions and determine if they are arbitrary, capricious, or not i n accord with the law. 5 U.S.C. § 706(2)(A); see also Tourus Records, Inc. v. DEA , 259 F.3d 731, 736 (D.C. Cir. 2001). Its basic legal tenets a re longstanding and clear. In determining whether an action was arbitrary and capricious, a reviewing court “must consider whether the [ag ency’s] decision was based on a c onsideration of the relevant factors and whether there has b een a clear error of judgment.” Marsh v. Or. Nat. Res. Council , 490 U.S. 360, 378 (1989) (internal quot ation marks and citationomitted). At a minimum, the agency must have considered rel evant data and articulated an ex planation establis hing a “rational connection between the facts found and the choice made.” Bowen v. Am. Hosp. Ass’n , 476 U.S. 610, 626 (1986) (internal quotation marks and citation omitted) ; see also Pub. Citizen, Inc. v.
FAA , 988 F.2d 186, 197 (D.C. Cir. 1993) (“The requirement that age ncy action not be arbitrary or capricious includes a require ment that the agency adequately explain its result.”). An agency action usually is arbi trary or capricious if: the agency has relied on factor s which Congress has not intende d it to consider, entirely failed to consider an important aspect of the problem, offered an explanation fo r its decision that runs coun ter to the evidence before the agency, or is so implausible that it co uld not12 be ascribed to a difference in view or the product of agency expertise. Motor Vehicle Mfrs. Ass’n of U.S. v. State Farm Mut. Auto. Ins. Co. , 463 U.S. 29, 43 (1983). As the Supreme Court has explaine d, “[t]he scope of review under t he ‘arbitrary and capricious’ standard is narrow and a court is not to substitute its judgmen t for that of the agency.” Id

. Rather, agency action is normally “entitled to a presumption of regularity.” Citizens to Pres. Overton Park, Inc. v. Volpe , 401 U.S. 402, 415 (1971), abrogated on other grounds by Califano
v. Sanders , 430 U.S. 99 (1977).
D. Jurisdiction and Venue The Court has federal question jurisdiction, see 28 U.S.C. § 1331; 5 U.S.C. § 500 et seq ., because this lawsuit arises unde r a federal statute. Venue is proper because Plaintiffs and the Department of Agriculture, A PHIS’s parent agency, reside inthe District of Columbia and a substantial part of the events at issue occurre d in the Distric t. See 28 U.S.C. § 1391(e)(1); see also Dehaemers v. Wynne , 522 F. Supp. 2d 240, 248 (D.D.C. 2007); Hunter v. Johanns , 517 F. Supp. 2d 340, 344 (D.D.C. 2007).
III. ANALYSIS
A. Motion to Dismiss Defendants begin by moving to dismiss Counts I and III, pertain ing to duplicative charges and the legality of th e reserve account respectively, a s time-barred. Defendants argue that its fee division between pa ssengers and aircraft and its m aintenance of a reserve account are both long standing and that Plain tiffs did not complain about e ither within six years of their origination, which is required t o bring civil actions against the United States. See 28 U.S.C. § 2401(a). Specifically, Defendants argue that the final agenc y action that resul ted in separate fees for passengers and commerci al aircraft occurred in 1992, a lmost 25 years ago, and APHIS13 has included a funding for a res erve in its fee calculations si nce an interim rule in 2002 which was finalized in 2003. Defendants contend that the 2015 rulema king never considered or addressed either established pr inciple and therefore did not re open them for new objections or restart the statute of limitations. Not surprisingly, Plaintiffs disa gree. They argue that the Rul e represented new agency action and they can object to all parts of it, even if s ome portions were not revised or reevaluated in 2015. It is clear that any challenge t o a final agency action must be made within 6 years.
See 28 U.S.C. § 2401(a). When a pre-ex isting rule or policy is ch allenged, the “re-opening doctrine” governs whether it is reviewable. “[W]here an agency ’s actions show that it has not merely republished an existing rule in order to propose minor c hanges to it, but has reconsidered the rule and decided to keep it in effect, c hallenges to the ru le are in order.” Public Citizen v. Nuclear Regulatory Comm’n , 901 F.2d 147, 150 (D.C. Cir. 1990). To determine whether an agency reconsidered a rule, a court look[s] to the entire context of the rulemaking including all r elevant proposals and reactions of the agency to determine whether an i ssue was in fact reopened. If in proposing a rule the agency uses language that can reasonably be r ead as an invitation to commen t on portions the agency does not explicitly propose to change, or i f in responding to comments the agency uses language that shows that it did in fact reconsider an issue, a renewed challenge to the und erlying rule or policy w ill be allowed. Id . However, a commenter cannot f orce an agency to reopen an iss ue by offering an unsolicited comment and getting a response. “ [A]n agency does not reopen arulemaking or policy determination ‘merely by respondi ng to an unsolicited comment b y reaffirming its prior position,’” CTIA v. FCC , 466 F.3d 105, 110 (D.C. Cir. 2006) (quoting Kennecott Utah Copper Corp. v. Dep’t of Interior , 88 F.3d 1191, 1213 (D.C. Cir. 1996)), or “by responding to a14 comment that addresses a settle d aspect of some matter, even if the agency had solicited comments on unsettled aspects of the same matter.” Kennecott , 88 F.3d at 1213. In its initial report, Grant Thor nton explained that it was ret ained to “conduct a comprehensive fee review to determine the full cost of AQI serv ices, identify potential changes to the fee structure, and reco mmend new fees.” Oct. 2011 GrantThornton Rep. at AR414; see also Proposed Rule at AR10 (“APHIS recently conducted a comprehensi ve fee review to determine the current cost of s pecific AQI services supported b y these fees.”); Sept. 2012 GAO Rep. at AR70277 (“In October 2010, A PHIS hired a contractor to conduct a comprehensive fee review to determine the full co st of AQI services, identify pot ential changes to the fee structure, and recommend new fees.”). Consiste nt with these statements, t he 2014-2015 AQI rulemaking was not simply a change in fee amounts, but constituted a whole sale re-evaluation of the system used to evaluate costs and determ ine fees, with the introductio n of a new methodology. Grant Thornton evaluated the entire st ructure of the AQI fee system a nd made recommendations for significant changes in an effort to recoup the actual costs of the services provided to each user class. For example, Grant Thornton recommended ending the AQI fee cap for maritime vessels and railcars, see May 2012 Grant Thornton Rep. at AR639-640, and appeared to rec ommend moving from a fee system under which passengers paid a fee and the aircraft on which they flew paid a separate commercial fee, to a fee system under which pas sengers paid a fee that covered their plane and only str ictly-cargo aircraft paid a commercial fee. Compare March 2012 Grant Thornton Rep. at AR498 (chart id entifying the pre-2015 fee sche me and including inspection of passenger aircraft with commercial aircraft fee) with id . at AR501-502 (Grant Thornton15 proposals that included passenger aircraft inspection in the pa ssenger (Air Pax) fee). 2 These charts show that so-called “duplic ative charges” (“passenger fe e” and “commercial aircraft fee” levied on all passenger aircraft) were considered during the AP HIS rulemaking. There is thus no time bar to Plaintiffs’ argume nts about duplicative fees. Evaluation of whether the authority to fund a reserve account w as “re-opened” by the 2015 rulemaking proves more diff icult. APHIS argues that i t did not reopen any aspect of the reserve account in the 2015 rul emaking; therefore, Plaintif fs’ reserve claim is untimely and should be dismissed. Although APHIS publically stated that the purpose of the rulemaking was a “comprehensive fee review,” Grant Thornton did not appear to re-examine the need or reasons for a reserve account. To the contrary, one of the explicit ca lculations by Grant Thornton addressed the appropriate am ount to fund the reserve and how to include it in the fees, but not whether it should be continued. See Oct. 2011 Grant Thornton Rep. at AR416-17 (“The next step was to determine what the reserve component of the total c osts should be. This amount was based on an estimate of the res erve . . . required to run the o perations of the AQI program for 3 months or 25% of the year. APHIS d ecided to build this reserve over three years, thus achieving the desired amount by FY2007.”); see also Proposed Rule at AR10 (“The proposed adjustments will also allow us to maintain t he AQI reserve account.”). The Court, however, evaluates “th e entire context of the rulema king” and finds that APHIS was not “merely republ ish[ing] an existing rule” wit h minor changes, but instead conducted an extensive review of the prior rule as a whole. Public Citizen , 901 F.2d at 150. The fact that Grant Thornton did notspecifically question the exis tence of a reserve account does not

2 The Court recognizes this reco mmendation, and the data upon wh ich it rests, is contested by the parties and discusses that challenge infra at section III.B.16 diminish the comprehensive nature of the 2015 rulemaking. Alth ough the question is a close one, the Court finds Plaintiffs’ reserve claim timely and will deny Defendants’ motion to dismiss.
B. Duplicative Commercial Aircraft Fee At the heart of their case, Pla intiffs argue that APHIS’s “deci sion to impose a separate commercial aircraft i nspection fee for arriving passen ger flights on top of the individual air passenger fee directly viol ates the plain language of the F ACT Act” and contradicts the conclusions of APHIS’s economic expert, Grant Thornton. Pls.’ Mot. at 19-20. Plaintiffs identify multiple concerns based on the FACT Act: (1) the stat ute directs that “[t]he costs of the services with respect to passenge rs as a class includes the cos ts of related inspections of the aircraft or other vehicle,” 21 U .S.C. § 136a(a)(2), which APHIS allegedly ignored; (2) consistent with the FACT Act, Grant Thornton recommended AQI fees of $4 pe r inbound air passenger and $225 per inbound commercial aircra ft and, in that calculation, defined “commercial aircraft” as those airplanes carrying only cargo, which APHIS ignored; and ( 3) APHIS does not adequately support its decision to charge both a passenger fee and a comme rcial aircraft fee on the same flight. Plaintiffs identify thr ee alleged inadequacies in APHI S’s explanation: (1) APHIS failed to justify treating air and seapassengers differently; (2) APH IS wrongly concluded that AQI inspection of passenger aircraft can be divided into “passenger ” inspections and “cargo” inspections; and (3) APHIS offe red no justificatio n for treatin g small passenger aircraft differently from large passenger aircraft. APHIS responds that the passenger fee and commercial aircraft f ee are not duplicative because the passenger fee covers aircraft inspectio ns that are rela ted to passenger flight, i.e. , the interior where passengers are located, associated waste a nd garbage, and passenger luggage, while the aircr aft fee covers the remaining costs of inspecti ng the exterior of17 the aircraft, its cargo, and cargo hold. APHIS acknowledges th at the costs may not be equal between inspecting a cargo-only aircraft and i nspecting the car go and hold of a plane that also carries passengers. APHIS expl ains the dichotomy by noting tha t it was required to determine a fee structure that charged each class of users for the services provided and that would be readily understood and predictable for the international air transport industry and its employees. In its consideration, APHIS weighed its ne ed to administer a clear fee structure against the probability that some passenger-and-cargo air craft may pay more than the st rict costs of the services related to the inspection of any individua l flight; it determined that the administrative problems and costs inherent in operating and auditing a fee schedule specifi c to each unpredicta ble variation of passenger-only, passenger-and-car go, and cargo-only aircraft ou tweighed the harm in overcharging some customers. As to Plaintiffs’ argument that Grant Thornton intended the “co mmercial aircraft” fee to be charged to cargo-only c ommercial aircraft, APHIS doub ts the weight of the accountants’ statements in their r eport. More critically, the agency argues Grant Thornton calculated the “commercial air craft” fee by dividing the total costs into the total number of international passenger and cargo aircraft, not the number of cargo-only aircraft. Theref ore, APHIS insists, despite any contrary language in Grant Thornton’ s reports, it is appropriately charging the $225 commercial airc raft fee to both passenger and cargo-only aircraft.
1. Division of costs in the FACT Ac t – What does the statute intend? Whether APHIS may charge both a “passenger fee” to those passen gers aboard an international flight and a “comm ercial aircraft” fee to the air line for AQI inspection services is dependent on the meaning of the t erm “related” in 21 U.S.C. § 1 36a(a)(2). Plaintiffs argue the passenger fee must cover the totality of costs related to inspe cting the vehicle (truck, bus, ship,18 airplane, etc.) in which they arr ive, while APHIS argues that p assengers are only required to pay for those AQI inspections that are related to their presence inthat vehicle. The FACT Act permits the Secretar y to “prescribe and collect fe es” to cover the cost of AQI services related to the arrival in the United State s of an “internati onal passenger, commercial vessel, commercial ai rcraft, commercial truck, or ra ilroad car.” 21 U.S.C. § 136a(a)(1)(A). The statute p rovides no definition of “commer cial aircraft” but APHIS has defined it to include “[a]ny air craft used to transport persons or property for compensation or hire.” 7 C.F.R. § 354.3(a). When setting fees, the Act requir es the Secretary to “ensure that the amount of the fees is commensurate with the costs of agricultur al quarantine and inspection services with respect to the cl ass of persons or entities payin g the fees,” and tha t “[t]he costs of the services with respect to pa ssengers as a class includes the costs of related inspections of the aircraft or other vehicle.” 21 U .S.C. § 136a(a)(2) (emphasis a dded); see also March 2013 GAO Rep. at AR70587 (“APHIS’s authorit y permits it to charge all pa ssengers for the cost of inspecting both passengers and the vehicle in which they arrive .”). When reviewing an agency’s interp retation of its enabling statu te and the laws it administers, courts are g uided by “the principles of Chevron U.S.A., Inc. v. Natural Resources Defense Council, Inc. , 467 U.S. 837 . . . (1984).” Mount Royal Joint Venture v. Kempthorne , 477 F.3d 745, 754 (D.C. Cir. 2007). Chevron established a two-step inquiry to guide the analysis. The initial question i s whether “Congress has direct ly spoken to the precise question at issue.” Chevron , 467 U.S. at 842. If so, then “that i s the end of the matter” because both courts and agencies “must give effect to the unambiguously expressed i ntent of Congress.” Id. at 842- 43. To decide whether Congress has addressed the precise quest ion at issue, a reviewing court applies “‘the traditional tools of statutory construction.’” Fin. Planning Ass’n v. SEC , 482 F.3d19 481, 487 (D.C. Cir. 2007) (quoting Chevron , 467 U.S. at 843 n.9). It an alyzes “the text, structure, and the overall statutory scheme, as well as the pro blem Congress sought to solve.” Id. (citing PDK Labs. Inc. v. DEA , 362 F.3d 786, 796 (D.C. Cir. 2004); Sierra Club v. EPA , 294 F.3d 155, 161 (D.C. Cir. 2002)). When t he statute is clear, th e text controls and no deference is extended to an agency’s interpre tation in conflict with the tex t. Chase Bank USA, N.A. v. McCoy , 562 U.S. 195, 210-11 (2011). If the statute is ambiguous or silent on an issue, a court proc eeds to the second step of the Chevron analysis and determines whether the agency’s interpretation is based on a permissible construc tion of the statute. Chevron , 467 U.S. at 843; see also Sherley v. Sebelius , 644 F.3d 388, 393-95 (D.C. Cir. 2011). Under Chevron Step 2 a court determines the level of deference due to the agency’s interpretation of the law it admi nisters. See Mount Royal Joint
Venture , 477 F.3d at 754. Where an “agency enunciates its interpretat ion through notice-andcomment rule-making or formal ad judication, [courts] give the a gency’s interpretation Chevron deference.” Id. at 754 (citing United States v. Mead Corp. , 533 U.S. 218, 230-31 (2001)). That is, an agency’s interpretation th at is permissible and reasonab le receives cont rolling weight, id. , “even if the agency’s reading diffe rs from what the court belie ves is the best statutory interpretation,” see Nat. Cable & Telecomms. Ass’n v. Brand X Internet Servs. , 545 U.S. 967, 980 (2005). An interpretation is pe rmissible and reasonable if it is not arbitrary, capricious, or manifestly contrary to the statute. Mount Royal Joint Venture , 477 F.3d at 754. Such broad deference is particularly warra nted when the regulation at issu e “concerns a complex and highly technical regulatory program.” Thomas Jefferson Univ. v. Shalala , 512 U.S. 504, 512 (1994) (internal quotation marks and citation omitted).20 The FACT Act states that passeng er fees must include “the costs of related inspections of the aircraft or other vehicle.” 21 U.S.C. § 136 a(a)(2). Plaintiffs want the Court to read “related inspections” to m ean all inspections of the vehic le, which would render aircraft passengers, but not the airline, f ully responsible for the cost of all inspections of the aircraft in which they arrived. However, Plaintiffs’ interpretation of the statute gives no meaning to the word “related.” If Congress intended passengers to pay in whol e for the inspection of the aircraft in which they arrived, the statute would say that passenger fee s must include “the costs of inspections of the aircraft. . . .” By inserting “related” an d using it to modify “inspections,” Congress specified that passenge rs are responsible only for the cost of inspecting their persons, belongings, and areas related to their presence on the flight, i.e. , such things as the passenger cabin and cabin waste and garbage . To give effect to the statu te’s limiting language, “related inspections” must be read as re ferring to inspections of person s, things, and areas that are related to passengers but nothing more. T hus, when CBP inspects the pa ssenger area of an aircraft, passengers must be charged its c ost but when CBP inspects cargo ( i.e. , non-passenger baggage) or non-passenger areas of the ai rcraft such as the cargo hold and exterior, the cost is unrelated to passengers and cannot be charged to them. Plaintiffs stress that less than 50% of arriving international passenger aircraft carries cargo and, therefore, t hose passenger-only flights do n ot require cargo-related AQI services and should not be charge d a commercial aircraft fee. APHIS explained, however, that even if a passenger aircraftdoes not have cargo onboard when i t enters the United States, it might well have carried cargo at some earlier point before ente ring the United States and AQI inspection is necessary to ensure that an invasive species or o ther contaminant was not dislodged from the cargo prior to entry. T he example cited at oral argum ent was a passenger aircraft that21 flew from Egypt to Paris and the n Paris to New York; even if th e aircraft carried no cargo on the Paris-New York leg, it could ha ve carried cargo from Egypt to P aris and picked up a contaminant. Therefore, CBP must conduct AQI on the entire air craft, not just the passengers and their luggage. See Agency Analysis of Proposed Rul e at AR40 (“All commercial airc raft, including international air pa ssenger carriers, air cargo carri ers, and air courier carriers, are subject to inspection and the com mercial aircraft user fee.”); Agency Analysis of Final Rule at AR287 (same); Final Rule at AR236 ( “All arriving international commercial flights are subject to the commercial airline clea rance fee and inspection.”). For the foregoing reasons, the C ourt finds the statute unambigu ously permits APHIS to charge both a “passenge r fee” and a “commercial aircra ft” fee for AQI services to inbound passenger airplanes. I t need go no further in its Chevron analysis. See Chevron , 467 U.S. at 842-43. If, however, the s tatute were deemed ambiguous , the Court also finds that the interpretation used by APHIS is reasonable and permissible unde r Chevron Step 2.
2. Grant Thornton’s analysis and proposed f ees – What constitutes a commercial aircraft? Plaintiffs argue further that even if two fees are permitted un der the statute, the fees proposed by Grant Thornton, and adopted by APHIS, were cal culated to charge a commercial aircraft fee only t o cargo aircraft and not to passe nger aircraft. By this reckoning, a commercial aircraft fee impose d on passenger aircraft is unnece ssary to recoup costs and is therefore inconsistent w ith the statute and APA. APHIS contracted with Grant T hornton to conduct a wholesale eva luation and review of the AQI fee program a nd to propose changes to the fee structure. The dr aft and final reports issued by Grant Thornton indicate that the accountants understood that passenger fees “should include the cost of relat ed inspections of the aircraft or other vehicle.” May 2012 Grant22 Thornton Rep. at AR630. Grant Thor nton also clearly recognized that the existing AQI fees had charged a “commercial aircraf t” fee to both passenger and cargo aircraft. See March 2012 Grant Thornton Rep. at AR498 (chart identifying the pr e-2015 fee scheme and indicating that the commercial aircraft fee was ch arged for inspection of passenger aircraft). When Grant Thornton proposed decreas ing the air passenger fee a nd increasing the commercial aircraft fee, its report appeared to indicate th at the air passenger fee covered inspecting the entirety of an air craft that carried passengers while the commercial aircraft fee was limited to cargo-only aircraft. See May 2012 Grant Thornton Rep. at AR638 (stating “revised air passenger fee includes the cost of inspecting passenger aircraf t”); id . (stating the commercial aircraft fee “now applies only to c argo aircraft because the co st of inspecting passenger aircraft is included in the air passenger fee”); see also March 2012 Grant Thornton Rep. at AR501-502 (Grant Thornton proposals stated p assenger aircraft inspection was included in passenger fee);
id . at AR484 (Grant Thornton differe ntiating between passenger an d cargo-only aircraft when assigning the costs of specific CBP activities to different use rs). Understandably, based on the language in Grant Thornton’s repor t, Plaintiffs argue that the $225 commercial aircraft fee should only be charged to cargo aircraft. APHIS agrees the language use d by Grant Thornton may suggest th at Grant Thornton intended the commercia l aircraft fee to cover only car go aircraft. However, APHIS delves into the data actuall y used by Grant Thornton, and publi shed in the Federal Register, to show that the Grant Thornton cal culation of the commercial airc raft fee included both passenger and cargo aircraft. In other word s, whatever the drafter of th e Grant Thornton report thought, the people with the green eyeshades w ho did the actua l calculation of the “commercial aircraft” fee divided the total cost of air craft inspections by 800,000+ inbo und aircraft per year to determine23 the commercial aircraft fee , that is, $225. The number of inbo und flights per year used in this calculation necessarily was the e stimate for the number of pass enger and cargo aircraft
combined , not merely cargo aircraft. Compare May 2012 Grant Thornton Rep. at AR638 (chart noting that Commercial Air (Ca rgo only) has a volume of 819,000 , or over 800,000 aircraft) with March 2012 Grant Thornton Rep. a t AR599-600 (listing the total number of commercial aircraft at just over 517,000 and total number of cargo aircraft at just under 140,000); see also Final Rule at AR237 (estimating in Table 4 the total number of commercial aircraft as 657,427 in FY10, 700,644 in FY11, and 719,251 in FY12). Because Grant Thornton used the projected total number of passenger and cargo aircraft to determine the per-aircraft fee, it is eviden t that the recommended fee was commensurate with the costs associated withinspections of all commercial aircraft despite contr ary statements in the report. Recognizing that the commercia l aircraft fee of $225 was derive d by dividing the total number of incoming passenge r and cargo aircr aft into the projected total inspection costs, APHIS reasonably determined tha t the fee should be charged to b oth. In reaching this conclusion, the Court finds that it is the agency’s decisions i n the Rule which ultimately govern, not the confusions in the consultant’s report.
3. The Final Rule – Does APHIS ade quately explain its rulemaking? Plaintiffs next argue that eve n if the FACT Act permits APHIS t o charge both a passenger fee and a commercial ai rcraft fee for AQI services, A PHIS has acted arbitrarily and capriciously in adopting a comm ercial aircraft fee of $225 with out proper explanation. Plaintiffs raise three specific issues: (1) APHIS sets passenger fees for cruise ship passengers to cover the entirety of its inspections of the ships, unlike air passenger fees; (2) it is unr easonable to divide AQI inspections of passenger ai rcraft between passengers and ca rgo; and (3) APHIS fails to address or explain why small and l arge passenger aircraft are t reated differently. Plaintiffs24 complain that APHIS failed to consider all relevant data and fa iled to establish a “rational connection between the facts found and the choice made.” Bowen , 476 U.S. at 626; see also Pub. Citizen , 988 F.2d at 197 (stating that agencies must adequately explai n the results of rulemaking). Are air passengers treated di fferently than sea passengers? The 2015 Rule added a new fee for passengers entering the Unite d States on a cruise ship and deleted the requi rement that cruise ships pay the commercial vessel fee applicable to other ships. See Final Rule at AR230, AR238, AR250. APHIS tracked its authority to charge a specific fee to passengers on cruise ship s to the FACT Act’s inclusion of “international passengers” and e xplained that it derived from t he unique nature of cruise ships, which are designed exclusively for passenger activities and notcargo. See id . at AR250. As a result, APHIS determined that the passenger fee for passengers on cruise ships should cover all costs associated with AQI inspections of passengers and the shi p. Plaintiffs argue that the same treatment should be extended to air passengers, so that air passengers pay the ent ire costs of inspecting passenge rs and aircraft. APHIS responds that the two passenger fees are similar because in both instanc es the cost of AQI services for passengers as a class includes the cost of related inspections of the aircraft or other vehicle. See Final Rule at AR 250 (“Based on our ABC analysis, we determined that the air passenger fee is not adequate to recover all the costs we incur in inspecting bo th passengers and aircraft, while the sea passenger fee is adequate to recover the costs we incur in inspecting both passengers and cruise ships.”); see also Proposed Rule at AR10. However, i n the case of aircraft, the c osts of inspections related to the passe ngers’ presence are not all of the AQI costs associated with a passenger aircraft ( see discussion in section III.B.3.b). For cruise ships, on the ot her hand, the25 sea passenger fee covers all inspections of the vessel itself b ecause all of the inspections are deemed to be related to the presence of cruise passengers on th e ship. The Court finds that APHIS reasonably determined that cruise sh ips do not carry cargo so that all associated inspe ction costs are properly attr ibutable to the passengers, while passenger aircraft may or may not carry cargo and, therefore, t he cost of AQI related to the aircraft itself is not exclusi vely attributable to the passenge rs. APHIS explained its conclusions and did not act arbitrarily and capriciously by setting inspect ions fees for cruise passengers and air passengers as it did. Are the fees for passengers and commercial aircraft covering th e same AQI inspections? The Proposed Rule explains what inspections are covered by the air passenger fee and what is covered by the commercial aircraft fee to justify c harging passenger aircraft both fees. Air passenger in spections include: prearrival analysis of incoming passengers and screening arrivi ng air passengers for agricultural products by CBP Agriculture Specialists and CBP Officers; ins pection of passenger baggage using CBP agriculture canines and specialized non-intrusive inspection equipment; inspecting the interior of the passenger aircraft; monitoring the storag e and removal of regulated international garbage from the a ircraft to ensure consistency w ith all regulatory requirements; safegua rding and appropriately disposi ng of any seized or abandoned prohi bited agricultural products; an d identifying pests found on prohibited agricultural products bro ught into the country by air passengers. Proposed Rule at AR15; see also Agency Analysis of Proposed Rul e at AR39 (“International air passenger inspections include the passengers, their baggage, an d the passenger areas of the aircraft (e.g., ensuring garbage compliance).”). The commercia l aircraft fee includes: reviewing manifests and docum entation accompanying incoming cargo; targeting higher risk cargo for inspection or clearance; inspecting various types of agricultural and agricultural-relat ed commodities, international mail, expedited courier packages,26 containers, compliant wood packaging material, and packing materials to screen for the presence of plant pests and contami nants, compliance with regulations, and determining entry status; inspecting the aircraft hold or exterior for contaminants, pest s, or invasive species; monitoring the storage and removal of regulat ed international garbage from the a ircraft to ensure consistency w ith all regulatory requirements; iden tifying pests found during inspect ion; and safeguarding shipments pending [Plant Protection and Quarantine] PPQ determination for treatment or final dispositio n. Proposed Rule at AR15. These de scriptions reasonably separate costs so that passengers pay only for searching passenger-relat ed areas, such as the cabin and the baggage area, while the airline pays for inspections of other areas of the plane, such as the cargo and cargo hold and the exterior of the aircraft. The Final Rule directly addressed co mments about the potential for duplicative fees: “We do not agree with the suggestion by the commenters that we are double charging or violating the FACT Act by imposing both an aircraft fee and an air passenger fee, since the respective fees cover different costs.” Final Rule a t AR250 (repeating the lists of separate costs for passenger and a ircraft inspections included in the Proposed Rule and quoted above); see also id . at AR234 (“APHIS can include the cost of inspecting commercia l aircraft that carry passengers in the int ernational air passenger user f ee if those costs directly relate to passenger baggage or regulated g arbage. APHIS does not include the cost of inspecting cargo or the cargo hold area of the plan e in the passenger fees. The co mmercial aircraft user fee pays the costs of inspecting the aircra ft itself, cargo inspection, the cargo hold, and the costs of monitoring aircraft disinfection.”); Agency Analysis of Final Rul e at AR284-85 (“International air passenger inspections incl ude the passengers, their baggage , and the passenger areas of the aircraft.”);. Plaintiffs challenge the agency ’s ability to divide inspection costs between passenger-related area s and the remainder of the aircraft, spec ifically noting the overlap between the “baggage area” and the “cargo hold.” Despite Plaintiffs’ a rgument that APHIS cannot27 adequately separate the relevant costs, it is evident from Gran t Thornton’s analysis, the statements in the Final Rule, and APHIS’s history of setting ai r passenger and commercial aircraft fees, that the agency ha s long set separate fees to co ver the particular costs associated with each user class and that inspections related to passengers require different AQI services than inspections of aircraft. APHIS explained the difference as lon g ago as its 1992 Rulemaking when faced with a similar challenge, noting that: [p]assengers pose a different ris k of bringing foreign diseases and pests into the United States than do the aircraft and cargo it carries. For example, passengers may have walked through dirt infested w ith parasites, or they may be carrying infested fruits or vegetable s or infected meat on their person or in their baggage. Aircraft ma y be infested with a pest which has escaped from infested cargo. Ai rcraft or cargo may need to be fumigated or disinfected. Also, passen gers are responsible for themselves and their baggage; the airline i s responsible for the aircraft and the cargo. For all these reas ons, passengers and their baggage must be inspected separately and i n a different manner than the aircraft and its cargo. 57 Fed. Reg. 755, 763-64 (Jan. 9, 1992). In every rulemaking s ince 1992, APHIS has made the same distinctions in fees, by which it charged passengers for their related searches and charged the commercial aircraft fee for the remainder. Plaintiffs poin t to no specific flaws in Grant Thornton’s ABC analysis and do not dispute the agency’s long pr actice. The Court finds no reason to doubt the sufficiency of Grant Thornton’s analysis or APHIS’s explanation that different types of inspections a re conducted for passenger-rela ted costs and commercial aircraft costs. As indicated above, the d ifferences are required by the statute and have been reasonably explained. Is it reasonable for APHIS to treat small and large passenger a ircraft differently? Finally, Plaintiffs contend that A PHIS acted in an arbitrary an d capricious manner by treating small passenger aircraft differently from large pas senger aircraft in the Rule and not28 charging small aircraft the comme rcial aircraft fee unless they actually carry relevant materials. APHIS maintains that its treatme nt of small aircraft is consist ent with other inspection regimes by the federal government and is reasonable. See Final Rule at AR236 (“APHIS maintains the 64-seat plane size distincti on in harmony with CBP and other U. S. Government agencies with jurisdiction over ci vil aviation.”). “Under [7 C.F.R.] § 354. 3(e)(2)(iv), all pa ssenger aircraft ori ginating in any country that have 64 or fewer sea ts and that do not carry certa in regulated articles are exempt from paying the aircraft AQI user fee.” Id . While the initial 1992 Rule included an exemption for aircraft with 30 seats or less, on March 17, 1993, APHIS ex panded that exemption to aircraft with 64 or fewer seats, see 58 Fed. Reg. 14305, 14305 (March 17, 1993), recognizing that t hose aircraft “require little or no inspection.” Id . However if a small aircra ft is carrying “[f]resh fruits, fresh vegetables, pla nts, unprocessed plant products, c otton or covers, sugarcane, or fresh or processed meats,” or offers a“meal service other than bever ages and prepackaged snacks” that contains “meats derived f rom ruminants, swine, or poultry or fresh fruits and fresh vegetables,” then a small aircr aft will require AQI inspection and will be charged the commercial aircraft fee. 7 C.F .R. § 354.3(e)(2)(iv). Plaintiffs argue that the same di stinction can be applied to large passenger aircraft. However, Plaintiffs do not dispute that a large pass enger aircraft might not have cargo when it arrives in the United States, but may have carried carg o on a prior leg of its trip and thereby contain contaminants. I t is, therefore, not unreasonab le for APHIS to require inspections unrelated to passengers for lar ge passenger aircraft on all inb ound flights but not all smaller aircraft.29 APHIS contends that the exempti on for small aircraft is consist ent with the intent and instructions of the FACT Act to charge users only for the a ctual services they receive. Under this command, because small aircraft do not require the s ame AQI services as large aircraft, they are properly exe mpted from a mandatory inspectio n payment for all flights. Additionally, APHIS notes the com plexity and admi nistrative inc onvenience of developing a range of commercial aircraft fees to distinguish between small and large aircraft, passenger and cargo aircraft, and passenger airc raft with or without cargo ona specific inbound leg; it argues such a regime would be unnecessarily burdensome and is not requ ired by the FACT Act. See Final Rule at AR236 (“APHIS and CBP save resources and costs by not having to design a process for administering a co mplex fee structure. This helps to keep the fee costs to the payer as low as possible. . . . [I]t would be administratively burde nsome to charge and audit a multitude of fees for the many different types of commercial ai rcraft and their cargo that enter the United States.”). The Court finds the continuati on of APHIS’s long -standing decis ion to exempt small passenger aircraft from automatic commercial airline insp ection fees on all flights was fully detailed by APHIS and is not a rbitrary or capricious or i n violation of the FACT Act.
4. Conclusion Despite some clear inconsistenc ies in understanding and the lan guage used by Grant Thornton and APHIS itself in the Rule, the Court finds AP HIS used Grant Thornton’s ABC analysis (which combined pa ssenger and cargo aircraft) to s et fees commensurate to the costs associated with the air p assenger user class and the comm ercial aircraft user class. Summary judgment will be grante d in favor of APHIS on Count I.30 C. Reserve Account Plaintiffs argue that APHIS vi olates the express language of th e FACT Act by using a portion of the AQI fees to fund a “reserve account” sin ce the authority to do so was expressly revoked by Congress af ter FY02. APHIS responds that the cited language, from the 1996 amendment to the FACT Act, di d not revoke the agency’s abi lity to fund a reserve after FY02, but only specified that the re serve was to be maintained in a Treasury account from FY96 to FY02 as APHIS transitioned from appropriated funding for AQI inspections to a fully selfsupporting funding module, after whi ch Agriculture would mainta in the fund in its own accounts. APHIS also argues that if the Court finds the FACT A ct ambiguous with respect its authority to fund a reserve acc ount after FY02, it should defer to the agency’s interpretation under Chevron

. See 467 U.S. at 842-43. As established in 1990, the FACT ACT stated: The Secretary shall adjust the amount of the fees to be assesse d under this subsection to reflect t he cost to the Secretary in administering such subsection, in carrying out the activities at ports in customs territory of the United States and preclearance and preinspection site outside the c ustoms territory of the United States in connection with the provision of agricultural quarantine inspection services, and in maintaining a reasonable balance in the Account. § 2509(a)(4). The most recent relevant amendment to the FACT A ct was enacted in 1996 and amended the fee author ization to state: (1) Fees authorized The Secretary of Agriculture may prescribe and collect fees sufficient— (A) to cover the cost of providing agricultural quarantine and inspection services in connection with the arrival at a port in the customs territory of the United States, or the preclearance or preinspection at a site outside the customs territory of the Un ited31 States, of an international passenger, commercial vessel, commercial aircraft, commerc ial truck, or railroad car; (B) to cover the cost of adminis tering this s ubsection; and (C) through fiscal year 2002, to m aintain a reasonable balance in the Agricultural Quarantine Inspection User Fee Account established under paragraph (5). 21 U.S.C. § 136a(a). Paragraph (a)(5) described the account cr eated at the Treasury: (5) Agricultural Quarantine Inspection User Fee Account. (A) Establishment. There is established in the Treasury of the United States a fund, to be known as the “Agricultural Quaranti ne Inspection User Fee Account”, which shall contain all of the fe es collected under this subsection and late payment penalties and interest charges collected unde r paragraph (4) through fiscal y ear 2002. (B) Use of Account. For each of fiscal years 1996 through 2002 , funds in the Agricultural Quaran tine Inspection User Fee Accoun t shall be available, in such amounts as are provided in advance in appropriations Acts, to cover the costs associated with the pro vision of agricultural quarantine and inspection services and the administration of this subsect ion. Amounts made available under this subparagraph shall be available until expended. (C) Excess Fees. Fees and other amounts collected under this subsection in any of fiscal years 1996 through 2002 in excess o f $100,000,000 shall be available for the purposes specified in subparagraph (B) until expended, w ithout further appropriation. Id . § 136a(a)(5). The pertinent quest ion is whether the 1996 ame ndment prohibits APHIS from collecting fees to maintain a r easonable balance, or fund a res erve, after FY02.
1. Where does APHIS base its authority to fund a reserve account? When APHIS first establishe d the AQI user fees in 1991, it resp onded to comments questioning its authorityto set fees to cover AQI service costs, administration costs, and a reserve fund. APHIS stated that it “included administrat ive costs and a r eserve fund in [its] cost calculations” because the 1990 FACT ACT “provide[d] that [ it] may recover the cost of administering the user fee progr am through the fees collected. . . . [and] also allowed for a32 ‘reasonable’ balance in the AQI user fee account.” 56 Fed. Reg . 14837, 14841-42 (April 12, 1991). Since the 1996 amendment a nd the inception of the AQI f ee system, APHIS has based its authority to fund the reserve a ccount on the language in the st atute authorizing the Secretary to collect fees to maintain a reasonable balance. In the current rulemaking, APHIS continued its reliance on the “reasonable bala nce” language located at § 136a (a)(1)(C). See Final Rule at AR229 (stating that “user fees s hould recover the costs of: . . . [m]aintainin g a reasonable balance, also referred to by APH IS as a ‘reserve’”). Only duri ng this litigati on did APHIS concede that after 2002 the expr ess statutory authority in § 13 6a(a)(1)(C) to fund a reserve account had expired; in its Suppl ementary Response, APHIS now j ustifies funding the reserve as part of the cost of “administer ing the user fee program” under § 136a(a)(1)(B). Defs.’ Supp. Resp. Pursuant to Court Order (Defs.’ Suppl. Resp.) [Dkt. 32] a t 2. The APA requires an agency to provide its authority and reasoni ng during rulemaking and a court may only affirm a new rule based on the reasoning provided at the time. See Nat’l Fuel Gas Supply Corp. v. FERC , 468 F.3d 831, 839 (D.C. Cir. 2006) (“[T]he grounds upon which the agency acted in ex ercising its powers [must be] those upon which its action can be sustained.”); see also SEC v. Chenery Corp. , 318 U.S. 80, 95 (1943) (“We merely hold that an administrative order cannot be upheld unless the grounds upon w hich the agency acted in exercising its powers were thos e upon which its action can be s ustained.”). Based on the Chenery doctrine, APHIS’s reserve fee may only be sustained if it is a uthorized by the “reasonable balance” language in § 136a(a)(1)(C), because that is the ground upon which APHIS relied in the rulemaking that se t a fee amount for a reserve. Therefore, the Court does not evaluate or rule on the agency’s current argument that it has a uthority to fund a reserve under § 136a(a)(1)(B).33 2. Is the FACT Act language ambiguous? Since the original FACT Act in 1990, APHIS has had authority to collect fees to cover AQI services. The statute identified three categories of costs that the AQI fees were to cover: (1) administration of the subsection, (2) costs in carrying out the AQI ac tivities, and (3) maintenance of a reasonable balance in the account. See § 2509. The phrase “maintain a reasonable balance” was underst ood to authorize APHIS to create a reserve fund. In 1996, the FACT Act was amended to create a true user fee account that was held by the Department of the Treasury until after FY02. The new amendment established a use r fee account at Treasury until after FY02 and described how it was to be used: (B) Use of account. For each of fiscal years 1996 through 2002 , funds in the Agricultural Quaran tine Inspection User Fee Accoun t shall be available, in such amounts as are provided in advance in appropriations Acts, to cover the costs associated with the pro vision of agricultural quarantine and inspection services and the administration of this subsection. Amounts made available unde r this subparagraph shall be available until expended. 21 U.S.C. § 136a(a)(5). At the e nd of FY02, the funds were to be transferred to the Department of Agriculture: After September 30, 2002, the unobligated balance in the Agricultural Quarantine Inspection User Fee Account and fees an d other amounts collected under this subsection shall be created to the Department of Agriculture accounts that incur the costs associa ted with the provision of agricultural quarantine and inspection se rvices and the administration of this subsection. The fees and other amounts shall remain available to the Secretary until expended without fiscal year limitation. Id . § 136a(a)(6). The 1996 amendment also changed th e statute’s language pertaini ng to fees the Secretary was authorized to collect. Compare § 2509(a)(4) (“maintaining a reasonable balance in the Account”) with 21 U.S.C. § 136a(a)(1)(C) (permitting fees to be set “through fiscal year34 2002, to maintain a reasonable balanc e in the Agricultural Quar antine Inspection User Fee Account established under paragraph (5)”). APHIS originally argued here that the time limit set in § 136a( a)(1)(C) was meant only to refer to the department that held the reserve account, i.e. , Treasury in FY96-FY02 and Agriculture after th e transition per iod. Now, in its written r esponse to a question posed at oral argument, APHIS concedes that th e specific language in the 1996 amendment that referenced maintenance of a reasonable balance expired after FY02. See Defs.’ Suppl. Resp. at 2 (“As part of [the 1996 amendment], the FAC T Act removed the language in the statute that the Secretary ‘shall adjust the amount of f ees . . . to reflect the cost to t he Secretary . . . in maintaining a reasonable balance in the’ accoun t.”). The Court agrees that § 136a(a)(1)(C) does not give APHIS current authority to charg e user classes to maintain a re serve account. APHIS may set AQI fees to maintai n a reasonable ba lance only if it provides a reasonable interpretation of the statute that provides that aut hority. 3 In the 2014-15 rulemaking, APHIS relied on the “reasonable balance” allowance in § 136a(a) (1)(C), but that expired after FY02. Whether there is authority to be found elsewhere, relian ce on expired statutory language was unreasonable and therefore arbitrary and capricious. The C ourt will grant summary judgment to Plaintiffs on Count III and remand this part of the rulemaking for further consideration and possibl e rulemaking by APHIS.

3 A March 2006 GAO Report did not e xpressly identify maintenance of a reasonable balance as an authorized fee. See March 2006 GAO Rep. at AR69981 (“The FACT Act authorizes user fees for (1) providing AQI services f or the conveyances, cargo, and passengers listed above; (2) providing preclearance or preinspe ction at a site outside the c ustoms territory of the United States to international airline passengers, commercial vessels, commercial trucks, commercial railroad cars, and commercial ai rcraft; and (3) administering the AQI user-fee programs.”).35 D. Cross-Subsidization Plaintiffs also argue that the Rule expressly violates the FACT Act requirement that the fee charged must be com mensurate with the costs of the services provided to each particular class of persons or vessels. In this challenge, Pla intiffs make two contentions. First, they argue that APHIS uses the fees charged to commercial passe nger aircraft to cross-subsidize services provided to other classes of vessels. Plaintiffs spec ifically challenge the fact that some classes of vessels are charge d no AQI fee, but still receive AQ I services upon entering the United States ( i.e. bus passengers, rail passengers , and private vehicles). Plain tiffs also contend that APHIS’s maintenance of a singl e reserve fund leads to cross-sub sidization and is a direct violation of the statute. APHIS responds that the Rule specifi cally addressed the issue of crosssubsidization and tha t the agency’s use of the ABC methodology to determine the AQI fees was intended to avoid any class of user s paying for inspections of another class. APHIS explains that the ABC methodology resulted in f ees directly linked to the cos ts attributable to each user class and inspection of the users that are not charged AQI fees is fu nded exclusively through CBP appropriations. APHIS further ar gues that a single reserve acc ount is appropriate as long as the reserve is funded through proportional contributions from each user class, which is why APHIS applies a 3% surcharge to eac h user class to fund the reserve. The FACT Act requires the Secret ary to “ensure that the amount of the fees is commensurate with the costs of a gricultural quarantine and insp ection services with respect to the class of persons or entitie s paying the fee.” 21 U.S.C. § 136a(a)(2). The ABC method used by Grant Thornton and APHIS to s et AQI fees in the 2015 rulemak ing required linking expenses or costs borne by APHIS and CBP to each individual user class, regardless of whether a fee would ultimately be charged. For example, Grant Thornton attri buted costs to rail and bus passengers, but an AQI fee was not ultimately assigned to those users. See May 2012 Grant36 Thornton Rep. at AR642 (“Fees do not recover costs for other pa ssenger classes (bus and rail). These costs would be covered by CBP’s appropriation, as current ly done.”). Grant Thornton and APHIS explained that the goal insetting the AQI fee was to mak e it “commensurate with the costs with respect to the class of persons or entities paying t he fees. This [was] intended to avoid cross-subsidization of AQI services.” Id . at AR630; see also Proposed Rule at AR10. The AQI fees were not intended to cover every cost associated with insp ections of all user classes, because APHIS recognized that some user classes are funded through CBP appropriations. See March 2013 GAO Rep. at AR70579 (“APHIS has chosen not to charge some classes of passengers, and the collections of the AQI progr am as a whole do not equal tota l identified program costs.”). Plaintiffs cite Kevin Shea, APH IS Administrator, who spoke at an AQI Stakeholder Webinar on Januar y 13, 2015; Mr. Shea stated that A PHIS was not going to promulgate an interim rule thatwould lower the air passenger f ee from $5 to $4 because APHIS “could not operate this program if that revenue was immediately taken away.” Stakeholder Webinar at AR194. Plaintiffs use this quote to argue that APHI S knew it was cross-subsidizing other user classes with the hi gh fees from air passengers. The Court finds that Administer Shea’s statement is somewhat ambiguous but could be read to admit that the pre-2015 fees resulted in cross-subsidization. However, s uch a conclusion does not implyor prove that there was an error in calculating AQI fees in the 2015 Rule. To the contrary, Adm inister Shea’s comment can be understood as saying that a revis ion to the fee structure was n ecessary to bring the system into compliance with the requirement t hat fees be commensurate with the costs of inspection for each user class. Altering just the passenger fee, before bringing a ll fees to the new rates determined through ABC analysis, would logica lly lead to a shortfall in re venue.37 The Court rejects Plaintiffs ar gument that APHIS improperly cro ss-subsidizes costs by using AQI fees from one us er class to pay for inspecti ons of users not charged AQI fees. It is clear from the record, and A PHIS’s repeated explanations during notice and comment, see Final Rule at AR229-31, 233, 238, that AQI fees were set using the ABC analysis and that services provided to those user s not charged an AQI fee are fun ded through normal CBP appropriations. Separately, Plaintiffs’ argue tha t the way APHIS uses money in the reserve account violates the prohibit ion on cross-subsidization. Plain tiffs focus on § 136a(a)(6), which states that the fees should be sto red in “Department of Agricul ture accounts,” and contend that the reference to multiple “accounts” requires APHIS to establis h separate reserve accounts for each user class. APHIS rejects t his analysis and notes that th e proceeds of all fees were once lawfully held in a single consolidated account at Treasury, whi ch indicates that Congress did not intend the “commensurate” requir ement to extend to the ultimate use of reserve funds. The FACT Act states that APHIS m ust ensure that the amount of the fees charged is commensurate with the costs of the particular user class, bu t does not specify that APHIS may only use fees collected from one user class on inspections of t hat user class. Section 136a(a)(2) of the Act instructs the Secr etary on how to set the fees, not how to use the money once it has been acquired. See 21 U.S.C. § 136a(a)(2) (“In setting the fees under paragraph (1 ), the Secretary shall ensure that the amount of the fees is commensur ate with the costs of agricultural quarantine and inspection service s with respect to the class of persons or entities paying the fees.”). GAO has commented on the f lexibility provided to APHI S to use fees as it deemed necessary as long as they are set“commensurate with the costs of services with respect to a particular pathway.” March 2013 GAO Rep. at AR70579 (“Once rev enue is earned from one38 pathway, however, it may be spent on any AQI-related program co st.”). The 2015 rulemaking clearly stated that fees were se t separately for each user clas s. See Final Rule at AR229. The reserve account is funded by a proportional percentage increase in the fee charged to all user classes. See id . at AR234 (“To fund the reserve, th e[] base fees are increased by 3.5 percent.”). Proportional funding is consistentwith the commensurate requir ement in the Act. The Court, therefore, finds that APHIS’s ma intenance and use of the reserv e fund as a single account does not violate the FACT Act and wil l grant summary judgment in fav or of the agency on Count II.
E. Lack of Meaningful Opportunity to Comment Finally, Plaintiffs challenge t he procedures of the 2015 rulema king, alleging that APHIS failed to disclose the dataunderlying its decisions to a lter the AQI fees until after the Rule was issued, and that APHIS relied on unreliable data in se tting the fees in the 2015 Rule.
1. Did APHIS Fail to Provide the Underlying Data? Plaintiffs argue that by fai ling to provide the data upon whichGrant Thornton relied in its fee model, APHIS “ prevented stakeholders and the public from evaluating the agency’s fee-setting process” a nd providing meaningful comments on the results. Pls.’ Mot. at 36-37. APHIS counters that Plainti ffs raised all of the same c omplaints and concerns in their comments to the proposed rule , when the underlying data was notavailable, as they do in this litigation, when the underlying data is available. Therefore, it contends, Plaintiffs were not deprived of a meaningful opportunity to comment and APHIS did n ot violate the APA. The APA requires an agency to provide the public with a meaning ful opportunity to comment on a proposed rule a nd “offer reasoned responses to significant comments.” Shands
Jacksonville Med. Ctr. v. Burwell , 139 F. Supp. 3d 240, 261 (D.D.C. 2015); see also Dist. Hosp. Partners, L.P. v. Burwell , 786 F.3d 46, 56-57 (D.C. Cir. 2015). An agency is also requi red to “examine the relevant data and art iculate a satisfactory explan ation for its action.” Dist. Hosp.39 Partners , 786 F.3d at 56-57. In order to satis fy the requirement that the public be provided a meaningful opportunity to comment , an agency must “identify and make available technical studies and data that it has e mployed” in developing a proposed rule. Connecticut Light & Power Co. v. Nuclear Regulatory Comm’n , 673 F.2d 525, 530 (D.C. Cir. 1982); see also Time
Warner Entm’t Co. v. FCC , 240 F.3d 1126, 1140 (D.C. Cir. 2001) (“[ A]n agency cannot res t a rule on data that, in critical degree, is known only to the age ncy.”). APHIS and Grant Thornton explaine d the process for determining the relevant fees for each user fee as ABC. ABC uses a two-step methodology to assign an organization’s cos ts to its work activiti es and then to its related outputs. . . . In the first step of ABC, we assigned costs to activities using resource drivers, which typically represent a cause-and-effect relationship to establish how muc h of a resource is consumed by each activity. . . . In the second step, we assigned APHIS and CBP activity costs to the outputs produced by performing the activities. Proposed Rule at AR12. Plainti ffs (and other commenters) compl ained that “because the cost data provided by APHIS did not provid e specifics regarding the calculation of the individual user class fees, the valid ity of the cost calculations overall is qu estionable” and “the lack of transparency unfairly inhibits [ the] industry’s ability to resp ond knowledgeably” to the proposed rule. Final Rule at AR230. In res ponse to such comments, APHI S provided a website link where applicable data was locat ed and provided more cost inform ation by user class in the text of the final rule. See id . Plaintiffs argue, however, th at the data provided with the p roposed rule and at the website did not include the lengthier r eport drafted by Grant Thornton on March 30, 2012, see March 2012 Grant Thornton Rep. a t AR432-AR624, or the User Fee Modeling Data40 utilized by Grant Thornton t o conduct the ABC analysis. See User Fee Modeling Data at
AR656-AR69963. It is undisputed tha t the March 2012 Grant Thornton Report and User Fee Modeling Data were not provided to the public during the rulema king, however, Plaintiffs have failed to demonstrate harm from that fact. APHIS argues, and t he Court agrees, that Plaintiffs have not raised significantly di fferent arguments or objections to the Rule after acquiring the data, therefore nullifying any ar gument that they were deprived of a meaningful opportunity to comment during the rulemaking period. Additionally, the only h arm Plaintiffs identified at oral argument was the harm of being subject to an AQI fee that they believed was improper under the statute, but that harm is not pa rticular to the data issue and is fully addressed by the arguments above which challenge numerous alleged infirmities in the Rule. The Court finds that although some data was not publicized during rulemaking, Plaintiffs have not shown any way in which they were prevented from enga ging in meaningful notice and comm ent or would have changed their position during the rulemaking.
2. Was the data used to determine fees fatally flawed? Plaintiffs also take issue w ith the data used by Grant Thornton and APHIS to determine AQI fees, arguing (1) the accountants improperly reli ed on a single year’s data and (2) the workload and labor data were highly unreliabl e. APHIS resp onds that an agency’s judgment about what data to use should rec eive an extreme degree of defe rence because agencies are “afforded wide latitude to determ ine whether particular data ma y be relied upon.” APHIS Opp’n at 39. In responding to Plaintiffs’ sp ecific arguments, APHIS states that (1) data from FY10 and FY11 were used to set the revis ed AQI fees, and (2) APHIS acted reasonably in relying on the workload and labor dataavailable to it.41 Agencies must often conduct anal yses with imperfect data and ca n only be expected to do the best they ca n with the information available to them. See, e.g., Motor Vehicle Mfrs. Ass’n , 463 U.S. at 52 (“It is not infre quent that the available data do not settle a regulatory issue and the agency must then exercise its judgment in moving from the facts and probabilities on the record to a policy conclusion.”); Natural Res. Def. Council, Inc. v. EPA , 529 F.3d 1077, 1085 (D.C. Cir. 2008) (describing the agency’s efforts to evalu ate health risks caused by certain industrial chemicals despite “gaps in the data” by backfilling certain data points with “environmentally protective defaults”). The Court recognizes that an agency cannot be faulted for using the data available to it to the best of its ability, but must evaluate why limited data was available. The lack of adequate record-k eeping by CBP has been thoroughly documented by GAO and the DHS OIG and is not in dispute. See March 2006 GAO Rep. at AR69965 (noting that “because of weaknesses in the design of CBP’s new financia l management system, CBP was unable to provide APHIS with i nformation on the actual costs of the AQI program by user-fee type—for example, fees paid by int ernational air passengers”); id . at AR69999 (“Although CBP provided detailed cost informa tion by activity an d user-fee typ e to APHIS for fiscal year 2004, CBP provided only estimated cost in formation for fiscal year 20 05 because of a weakness in the design of the agency’s new financ ial management system.”); Feb 2007 OIG Report at AR70745 (indicating the data system used t o track agricultural inspecti on activities “continues to be a problem at CBP”); Feb 2008 GAO Rep. at AR70129 (“In the case of the AQI, customs, and immigration vessel and sea passe nger fees, the agencies and Con gress lack information on the total costs of the combined i nspections, and therefore do not k now whether fee collections cover the costs of the consolidated i nspection program.”); Sept 2012 GAO Rep. at AR70278-8042 (indicating that, although improve ment had been made to the dat a collection system, CBP still had issues with accurate data c ollection, including with data i nput inconsistencies between ports and lack of adequate review by managers); id . at AR70290 (“[T]he agencies may not have sufficient information on whic h to base key decisions to suppor t the AQI program because the data the two agencies are coll ecting and using for managing the program may not be reliable.”); March 2013 GAO Rep. at AR70578 (stat ing “data quality is an ong oing issue with AQI data systems”); id . at AR70580 (“CBP does not capture all time spent on agriculture activities in its Cost Management Information System (CMIS)—the system in which C BP tracks its activities and determines personnel costs. B oth to accurately set AQI fee rates to recover program costs and to allocate fee revenues be tween APHIS and CBP proportionat e with each agency’s program costs, CBP must accurately trac k its expenses related to the AQ I program.”); id . at AR70581 (“[A]t 31 ports and other locat ions, CBP did not charge any pri mary inspection time to agriculture-related CMIS codes for all or a portion of fiscal y ear 2012, which means that AQI costs at these ports are being understated.”). Although CBP continues to suffer fr om data challenges in tracki ng AQI services by user class, improvements have been made since the original G AO report in March 2006, and CBP continues to work to impleme nt an adequate system to track inspection costs. In September 2012 the GAO reported on improvements to CBP’s data system and noted that: CBP added agriculture-specific activity codes to its financial management system, which, according to CBP officials, allows CB P to provide APHIS with actual costs related to user fees. In ad dition, CBP issued guidance to clarify how employees should account for activities that are simultaneous ly related to immigration, cust oms, and agriculture activities so that this information could be tr acked for the purpose of collecting AQI user fees. According to APHI S and CBP officials, the new activity codes and guidance allow CB P to accurately report its costs b y user fee type to APHIS and en sure financial accountability for funds allocated to AQI user fees.43 Sept 2012 GAO Rep. at AR70267-68. GAO also noted that, despite the continuing issues with data collection, CBP and APHIS m ust use the data available to s et user fees. See March 2013 GAO Rep. at AR70578 (“Office of Management and Budget Circular A-25 states that when reviewing user fees, full cost s hould be determined or estimate d using the best available records of the agency, and new cost accounting systems do not need to b e established solely for the purpose of rate-setting. The cont ractor also solicited input f rom stakeholders as part of the fee review process, a practice cons istent with our User Fee Design Guide.”). Regardless of any continued inade quacies in the CBP data for di fferent types of AQI inspections, APHIS was requi red to set fees commensurate wi th the costs associated with providing AQI services to each us er class. To satisfy that req uirement, APHIS enlisted Grant Thornton to conduct an activity-b ased costing an alysis using th e best data it had available, data from FY10 and FY11. Although Plainti ffs argue that the data wa s insufficient and should not have been used to calculate the fees, they offer no alternative and provide no reason to believe data from other fiscal years w ould have been more reliable. Th e Court finds that APHIS used its judgment to determine that data from FY10 and FY11 were the bes t available and sufficient to calculate AQI fees and that j udgment should be given significan t deference. See Final Rule at AR241-42 (“APHIS and CBP identifie d the correct data to use in the model and eliminated the identified inconsistencies. Issu es such as these in a very lar ge operation are con tinuous in nature as the activities change, new sy stems become available, priorit ies change, or new demands for information arise. The data is r elevant and it is part of offi cial government systems. APHIS and CBP are continually working togeth er to enhance data collection .”); see also Oct. 2011 Grant Thornton Rep. at AR421 (“The workload (output) data received fr om both agencies is considered44 to be reasonably accurate.”). F or the foregoing reason, the Co urt will grant summary judgment to the agency on Count IV.
IV. CONCLUSION For the foregoing reasons, the Court will deny Defendants’ moti on to dismiss, grant summary judgment to Defendants on Counts One I, II, and I V, and grant summary judgment in favor of Plainti ffs on Count III. Rulemaking will be remanded to APHIS for reconsideration of its authority t o charge a surcharge for a re serve account. A memorializing Order accompanies this Opinion.

Date: March 28, 2018 /s/ ROSEMARY M. COLLYER United States District Judge