Lt. Col. William Helixon had urged that the most serious charges against Brig. Gen. Jeffrey A. Sinclair be dropped because they rely solely on the woman's accusation that he twice forced her to perform oral sex.
But those above the seasoned sex crimes prosecutor overrode him, rebuffing an offer from Sinclair to plead guilty to lesser charges.
Defense attorneys allege the top brass moved forward because they were worried about the political fallout that would result if the charges were dropped.
Helixon was pulled from the case after leading it for nearly two years, after a superior officer took him to a military hospital for a mental health evaluation, according to testimony.
Following a daylong hearing, a judge ruled the case should go to trial. Opening statements are set for Thursday.
"No offense to Lt. Col. Helixon, but I don't care what he thinks and neither should the court," Lt. Col. Robert Stelle, who replaced Helixon as lead prosecutor, told the judge.
The case against Sinclair, believed to be the most senior member of the U.S. military ever to face trial for sexual assault, comes as the Pentagon grapples with a troubling string of revelations involving rape and sexual misconduct within the ranks. Influential members of Congress are also pushing to remove decisions about the prosecution of sex crimes from the military chain of command.
Sinclair, the former deputy commander of the 82nd Airborne, has pleaded not guilty to eight criminal charges including forcible sodomy, indecent acts, violating orders and conduct unbecoming an officer and a gentleman. He faces life in prison if convicted of the sexual assault charges.
Lawyers for the married father of two have said he carried on a three-year extramarital affair with a female captain under his command during tours in Iraq and Afghanistan. The admission of an affair will almost certainly end his Army career.
In pretrial hearings, prosecutors have painted Sinclair as a sexual predator who abused his position and threatened to kill the accuser and her family if she told anyone of their relationship.
The Associated Press does not publicly identify the alleged victims of sexual assaults.
Helixon, who was described as dealing with "personal issues," wasn't called to testify Tuesday.
But among those called to the stand was Brig. Gen. Paul Wilson, a high-ranking military lawyer stationed at the Pentagon.
Wilson said another general sent him on the morning of Feb. 8 to check on Helixon, who was then staying in a room at the Ritz Carlton Hotel in Washington. He said he arrived to find Helixon appearing drunk and suicidal.
"He was in the midst of a personal crisis. He was crying. He was illogical," Wilson testified. "I truly believed if he could have stepped in front of a bus at the time, I think he would have."
The lead prosecutor had become convinced the accuser lied under oath when she testified in January about evidence collected from a cellphone.
The captain testified that on Dec. 9, shortly after what she described as a contentious meeting with prosecutors, she rediscovered an old iPhone stored in a box at her home that still contained saved text messages and voicemails from the general. After charging the phone, she testified she synced it with her computer to save photos before contacting her attorney.
However, a defense expert's examination suggested the captain powered up the device more than two weeks before the meeting with prosecutors. She also tried to make a call and performed a number of other operations.
Three additional experts verified those findings.
Wilson testified that Helixon was distraught that the accuser had lied to him.
"I served with him in combat in Afghanistan, making targeting decisions with people's lives on the line. I have never seen another human being in a state like that," he said.
Wilson said he took Helixon to the emergency room of a nearby military hospital at Fort Belvfor a mental health evaluation. Though a psychiatrist who interviewed the prosecutor declined to admit him for treatment, Wilson said he told Helixon's immediate superior back at Fort Bragg that the prosecutor was no longer fit to handle the case.
"He was not fit for any kind of duty. I would not have trusted him to drive a car," Wilson said.
In an unusual move, the defense called Richard Scheff, Sinclair's lead lawyer, to the stand.
Scheff testified that Helixon had confided in him that he was concerned the case had become too politicized.
"He said everyone on his team had reasonable doubt," Scheff said. "He said, 'I'm going to be the guy who gets hurt in this. I'm going to have a problem."
The defense introduced a December letter the military lawyer assigned to represent the accuser sent to Lt. Gen. Joseph Anderson, the commander at Fort Bragg. Under military law, it was up to Anderson to decide whether or not to accept Sinclair's plea offer.
Writing on behalf of the accuser, Capt. Cassie L. Fowler urged Anderson to reject the deal, suggesting that to do otherwise would "have an adverse effect on my client and the Army's fight against sexual assault."
"Acceptance of this plea would send the wrong signal to those senior commanders who would prey on their subordinates by using their rank and position, thereby ensuring there will be other victims like my client in the future," Fowler wrote.
Military judge Col. James Pohl said Fowler's letter to Anderson was improper, but did not constitute evidence of unlawful command influence. Anderson is a three-star general, the judge said, while the special victim's advocate is just a captain.
After the ruling, Sinclair's lawyer suggested that the Army was sacrificing Helixon's career and reputation to pursue a flawed case.
"Today's testimony was deplorable," Scheff said. "The government undertook a vicious character assault against someone they previously called their 'rock star' sex crimes prosecutor, because he was the only Army leader with the integrity to stand up to politics. People should be rewarded for honesty, not punished for it."
Follow Associated Press writer Michael Biesecker at http://www.twitter.com/mbieseck.