The two top lawyers at the military commissions at Guantanamo Bay are among 23 general officers whose billets are being eliminated in Defense Secretary Pete Hegseth’s continuing shakeup of top brass at the Pentagon.
They are:
- The Chief Prosecutor, a role currently occupied by Navy Rear Adm. Aaron Rugh, who has been on the job long enough to retire with one-star benefits.
- The Chief Defense Counsel position, now held by Marine Brig. Gen. Jonathan Vaughn, who has been head of the Military Commission Defense Organization since Dec. 31, 2025.
Those roles are being reduced to the rank of a military colonel or Navy captain, called 06, starting Jan. 1, according to the order signed by Hegseth on Sept. 16. They are the only two lawyer jobs on the list.
It was unclear whether the two men will be able to find other jobs in the Pentagon, or will retire. They will need to be replaced by military lawyers of the lower rank.
The Obama administration elevated the rank of the chief prosecutor with the appointment of Army Brig. Gen. Mark Martins in 2011. Then, for equity, the chief defense lawyer became a general with the appointment of Marine Brig. Gen. John Baker in 2015.
Elevation of those roles has long been credited with enhancing the clout of the military commission leaders, particularly their ability to get resources in the rank-conscious Department of Defense.
The timing of their departure coincides with the early phase of the first capital case at the Guantanamo military commissions. Jury selection is scheduled to start this month in the trial of Abd al-Rahim al-Nashiri, a Saudi man who is accused of conspiring in the Oct. 12, 2000 bombing of the USS Cole in the port of Aden, Yemen. Seventeen sailors were killed. The bulk of the trial is expected to take place in early 2027.
Rugh recently assigned Navy Cmdr. Clayton Trivett as lead prosecutor in the Cole case. Both Rugh and Trivett were key players in reaching plea agreements with three of the defendants in the 9/11 case in 2024, until former Defense Secretary Lloyd Austin revoked the agreements. The defendants Khalid Shaikh Mohammed, Walid bin Attash and Mustafa al-Hawsawi have petitioned the Supreme Court to hear their challenge to reinstate the plea deals.
The first one-star officers who ran the prosecution and defense offices had significantly higher-profile roles than the colonels and captains who preceded them, both inside the war court chamber and in public appearances.
In 2011 and 2012, Martins sat in court as lead prosecutor at the arraignments of six prisoners in the USS Cole and 9/11 cases, the war court’s only capital cases, and was part of the litigation team for years. He also traveled to law schools around the country to promote the military commissions and presided over press conferences at Guantanamo that included victims of terror attacks commenting on the proceedings. He was the longest-serving chief prosecutor and the subject of a 2013 profile by the ABA Journal, “Meet the man who would save Guantanamo.” He retired to private practice in Washington, D.C. in 2021.
Baker steered his defense organization through some of its most turbulent periods, which included the discovery of listening devices in attorney-client meeting rooms at Guantanamo prison. A military commissions judge also found him in contempt and confined him to his quarters for refusing to reinstate lawyers who quit in an ethics dispute. A federal judge vacated the conviction. He retired in 2021 and is now the federal public defender for Western North Carolina. His office has a Capital Habeas Unit, a regional office that represents people sentenced to death in state and federal courts in the Fourth Circuit.
