The suit additionally alleges that the conditions of detainment of these prisoners, as well as the length of detainment, violated their rights, as prisoners were held in the Administrative Maximum Special Housing Unit (ADMAX SHU); deprived contact with their attorneys, families, and friends; prevented from the practice of their religions; and treated inhumanely in various ways, including being verbally and physically abused.

[11][12] On December 18, 2009, a two judge panel of the Second Circuit affirmed in an unsigned per curiam decision, with Sotomayor not participating due to her elevation to the Supreme Court of the United States.

[13] The Second Circuit remanded to Judge Gleeson for further consideration under the new pleading standards created by Ashcroft v. Iqbal (2009), a separate case regarding conditions at the MDC.

[10] Plaintiffs eventually filed four amended complaints, incorporating by reference April[14] and December 2003[15] United States Department of Justice Office of the Inspector General reports investigating the abuses at MDC.

[19] On February 29 and April 1, 2016, Circuit Justice Ruth Bader Ginsburg granted the Solicitor General of the United States’s applications to extend the deadline to file a petition for a writ of certiorari.

[22]: 313  Calling that era an "ancien regime", the Court explained that it is now more mindful of separation of powers by looking for clear legislative intent before allowing claimants to seek damages.

Finally, the Court granted each defendant qualified immunity on the civil conspiracy claim, acknowledging without resolving the longstanding circuit split regarding the impossibility of conspiring within a single government department.

[22]: 317  Thomas also expressed concern about the precedents which establish the doctrine of qualified immunity, which he considered at odds with the common-law text of the statute and "substitute[s] our own policy preferences for the mandates of Congress.