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The prosecutor was willing to abandon the most serious charges despite believing Gen. Sinclair was guilty, a spokesman from her office said, proving that commanders are more aggressive than prosecutors when it comes to getting justice for the victims.

“The prosecutor believes that, as a tactical matter, the charges of sexual assault should be dropped in part because those charges would be difficult to win at trial,” Mrs. McCaskill’s office said in a statement. “If commanders could not launch courts-martial, the brigadier general in this case would likely be off the hook for an alleged sexual assault which both military commanders and prosecutors believe occurred.”

Several reforms championed by Mrs. McCaskill became law in last year’s defense bill, including eliminating the “good soldier defense” for sexual assault cases. That could have led to a different outcome in this case if it had been law, Mr. Jacob said.

The defense allowed commanders to consider a service member’s contributions to the military and good behavior when deciding whether to bring a case to trial and the outcome of the case. As a three-war veteran who contributed a lot to the military, Gen. Sinclair had an advantage over his accuser, who was a lower rank with less experience, Mr. Jacob said.

“If [the good soldier defense] had been in effect, it would have reshaped the lens through which the commander was viewing [Gen.] Sinclair with regard to charges,” Mr. Jacob said.

Some say the high-profile public debate over the Sinclair case is making the system worse.

“The military is held up as the horror show, but the fact is that the military is no better or no worse than the civilian system,” said Gary Solis, a former Marine judge advocate general who teaches at Georgetown University Law Center. “For every military law horror story that you read about or hear about, there are two or three from the civilian justice system.”

Mr. Solis said that worrying about who is able to convene a military trial misses the point.

“It’s causing people to focus on the wrong place, on the convening authority, as [Ms.] Gillibrand did. Changing who prosecutes the cases doesn’t even approach the problem. The problem is not who makes the court-martial happen; the problem is why the conduct happened,” he said. “Nobody wants to talk about that because it’s hard.”