[2][3] Frakt is notable for his appointment to defend Guantanamo detainee Mohammed Jawad, an alleged combatant facing charges for events that took place when he was a minor.

Frakt also represents another Guantanamo detainee who faced a military commission, Ali Hamza al-Bahlul, the alleged Al Qaida propaganda chief from Yemen.

"[2] The June 19, 2008, hearing where Frakt challenged Hartmann's participation and argued for dismissal of the charges based on torture and outrageous government conduct lasted 14 hours.

[2] According to Carol Rosenberg, of the Miami Herald, Frakt argued that Jawad had been subjected to: "...pointless and sadistic treatment [in a] bleak underworld of barbarism and cruelty, of anything goes, of torture.

"[10] Frakt also argued, during his challenge of Hartmann's unlawful influence, that the Prosecution had failed to release important records to the Defense, and that this showed that the process through which Jawad was charged was rushed and without proper preparation.

[11] According to Mike Melia, writing for the Associated Press, Henley ruled that Hartmann: "...compromised his objectivity in public statements aligning himself with prosecutors and defending the Pentagon's system for prosecuting alleged terrorists."

[2] Following previous inquiries into abusive treatment of detainees, this technique had reportedly been ordered discontinued two months prior to its use on Jawad by the then Commanding Officer of JTF-Guantanamo, Brig Gen Jay Hood.

[3] On July 11, 2008, in another filing submitted to the Military Commission Frakt reported that the Prosecution had withheld evidence of the medical effects on his client of the two weeks of sleep deprivation.

Frakt reported that the medical records showed that Jawad had lost ten percent of his body weight during his sleep deprivation, and that he had told doctors he had been urinating blood.

On August 7, 2008 an article in The Washington Post reported that newly published documents showed that the prohibited sleep deprivation technique had been in wider use than had previously been known.

At the August 13–14 hearing, an intelligence officer formerly stationed at Guantanamo testified that the frequent flyer program was "standard operating procedure" and was used on dozens of detainees until at least April 2005.

On September 21, 2009 historian Andy Worthington, author of The Guantanamo Files, published a letter from Frakt that documented the role he and his colleagues had hoped to play in Mohammed Jawad's re-integration into Afghan society.

[16] In the winter of 2012 Frakt published a one hundred and twenty page article in the University of Pittsburgh Law Review, entitle: Prisoners of Congress: The Constitutional and political clash over detainees and the closure of Guantanamo.