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In July 2013, a motion was filed seeking his release because his physical and emotional health had deteriorated to the point where he could not pose a threat. On October 3, 2013, Ben Fox, of the Associated Press, reported that the United States Department of Justice had dropped its opposition to Idris's repatriation.

On June 28, 2013, Cowan filed a motion which Carol Rosenberg, of the Miami Herald described as "a novel twist" in habeas petitions, in that it ignored assertions of the threat Idris posed, prior to his capture. The motion argues "he's too fat, too crazy and too physically sick to be a danger in the future. So Lamberth should send him home." Rosenberg notes the motion cites "Army regulations that recommend repatriation of POWs who are so sick they can't recover", and that the "Geneva Conventions require a war prisoner be sent home if his mental or physical fitness 'have been gravely diminished.'"

A July 2013 habeas corpus filing argued that he should be repatriated because he had health problems so severe that he could never pose a threat to the USA—even if he wanted to. Summarizing the report, Carol Rosenberg of the Miami Herald noted that he had been diagnosed with mental health problems shortly after his arrival in Guantanamo in 2002. He had since been diagnosed as having "schizophrenia, disorganized type." Rosenberg described how, when he was last scheduled to have a phone call to his habeas attorney, and was brought to the phone room, he was too confused to realize he should raise the phone's handset to his face.

Idris was transferred to Sudan on December 19, 2013.

On April 25, 2011, whistleblower organization WikiLeaks published formerly secret assessments drafted by Joint Task Force Guantanamo analysts. A ten-page assessment was drafted at Joint Task Force Guantanamo on April 15, 2008. That assessment was signed by camp commandant Mark Buzby and recommended his continued detention in Guantanamo. He was described as a "low threat" prisoner, which Carol Rosenberg, of the Miami Herald, explained meant he was compliant, and didn't represent a threat to JTF-GTMO staff. She reported the assessment "advised against his release, in part, because he 'resisted cooperation with interrogators and remains largely unexploited' — meaning he had yet to spill any al-Qaida secrets." She noted that the report described his health as "fair", completely skipping over serious mental and physical health issues that were made public in a July 2013 update to his habeas petition.

In 2009, shortly after he took office, United States President Barack Obama created a new Guantanamo Joint Task Force, with officials seconded from a range of Federal agencies, to conduct brand new assessment of captives' status. That review recommended that Idris be repatriated to Sudan.

Scholars at the Brookings Institution, led by Benjamin Wittes, listed the captives still held in Guantanamo in December 2008, according to whether their detention was justified by certain common allegations:

On June 12, 2008, the United States Supreme Court ruled, in Boumediene v. Bush, that the Military Commissions Act could not remove the right for Guantanamo captives to access the US Federal Court system. And all previous Guantanamo captives' habeas petitions were eligible to be re-instated.

On July 18, 2008, Jennifer R. Cowan of DEBEVOISE & PLIMPTON LLP re-initiated Civil Action No. 05-CV-1555 on behalf of Ibrahim Osman Ibrahim Idris.

His habeas petition was first filed before US District Court Judge James Robertson. In September 2007, the Department of Justice published dossiers of unclassified documents arising from the Combatant Status Review Tribunals of 179 captives, including Idris's.

On August 15, 2006, his case was amalgamated with al Qosi v. Bush, along with 130 others.

The Military Commissions Act of 2006 mandated that Guantanamo captives were no longer entitled to access the US civil justice system, so all outstanding habeas corpus petitions were stayed.

Originally, the Bush Presidency asserted that captives apprehended in the "war on terror" were not covered by the Geneva Conventions, and could be held indefinitely, without charge, and without an open and transparent review of the justifications for their detention. In 2004, the United States Supreme Court ruled, in Rasul v. Bush, that Guantanamo captives were entitled to being informed of the allegations justifying their detention, and were entitled to try to refute them.

Combatant Status Review Tribunal panel 13 convened on November 3, 2004, to confirm Mahmud Idris's "enemy combatant" status. A seventeen-page dossier of unclassified documents prepared for that tribunal was assembled for his habeas corpus attorneys.