WASHINGTON

UNTIL recently, no uniformed lawyer was viewed by the Obama administration with greater favor than Brig. Gen. Mark S. Martins, the scholarly chief prosecutor of the military commissions system who is leading the case against Khalid Shaikh Mohammed and four other Guantánamo Bay detainees accused of aiding the terrorist attacks of Sept. 11, 2001.

A Rhodes Scholar who graduated first in his class at West Point and earned a Harvard law degree alongside a young Barack Obama, General Martins served for five years in Iraq and Afghanistan, helped review detainee policies for President Obama in 2009, and was handpicked to reboot commissions in the hope that his image and conduct would persuade the world to respect the outcome of the Sept. 11 case — prosecutors are seeking death sentences — as legitimate.

But next week, when General Martins returns to public view at a pretrial hearing in the Sept. 11 case, he may appear to have gone rogue. He has engaged in an increasingly public dispute with the administration centered on an uncomfortable question he is refusing to drop: is it valid for the United States to use tribunals to charge idiosyncratic American offenses like “conspiracy,” even though they are not recognized as war crimes under international law?

General Martins’s standoff with the administration is writing a new chapter in a familiar narrative: since the 2001 terrorist attacks, military lawyers in the Judge Advocate General’s Corps have repeatedly clashed with politically appointed lawyers over the laws of war.