This week, Colonel Pohl stopped the court-martial, sent the jury home and offered General Sinclair another chance to try to hammer out a plea agreement, presumably on lesser charges. The military, in its pursuit of General Sinclair, seemed overly concerned about politics and its public image, he suggested.

Image Col. James L. Pohl, the judge. Credit... Associated Press

The breakdown of the prosecution’s case was unquestionably a black eye for the Army at a time when it has been trying to fend off criticism on Capitol Hill that it is unable to clamp down on sexual assault, which statistics show has risen steadily in recent years. General Sinclair’s court-martial took on special significance because he is possibly the first general to face sexual assault charges, and because his accuser was herself a promising junior officer.

But a review of the past three months suggests that the prosecution had doubts about whether a jury would believe the witness, an intelligence officer and Arab linguist who had worked with General Sinclair in both Iraq and Afghanistan, even before the January pretrial hearing. Though she told a compelling story of being bullied into sex, threatened and even physically abused by General Sinclair, the details of her story had shifted on some points, and, the defense said, she had claimed sexual assault only after it appeared she faced legal problems herself.

Other forces also played into the unraveling. Behind-the-scenes tensions among prosecutors and the captain and her special victim counsel complicated the prosecutors’ task, emails show. The job of special victim counsel is a new one, created to protect the rights of alleged sexual assault victims, and prosecutors seemed to clash with the captain’s counsel, even though they were expected to be allies.

General Sinclair was represented by high-powered, and expensive, private lawyers, in addition to military defense counsel. Financed in part by contributions from family and friends, the team effectively and aggressively undermined the prosecution’s case bit by bit.

Finally, the judge, who had handled some cases at the detention center at Guantánamo Bay, Cuba, seemed receptive to the idea that the prosecution had been improperly influenced by political concerns. Colonel Pohl’s decision to cite a military legal concept known as unlawful command influence in stopping the trial was relatively rare. But it highlighted the conflicted sentiments in the military over how best to combat sexual assault in the ranks.

A National Issue

When General Sinclair was first charged, in 2012, the Pentagon was already facing widespread criticism that senior officers had long failed to take sexual misconduct allegations seriously. On Capitol Hill, the Sinclair case became fodder in a Senate battle over how to overhaul military sexual assault prosecutions, with proponents and opponents of competing bills each arguing that the case, in all its convolutions, provided proof that their side was correct.