A sordid account involving illicit sex in uniform will be aired this week in an austere courtroom at Fort Bragg, N.C., and the results could tip the scales in a high-stakes debate in Congress over the future of the military justice system.

The defendant, Brig. Gen. Jeffrey A. Sinclair, is accused of carrying on a long affair with a junior officer and sexually assaulting her on two occasions, among other crimes. He is only the third Army general to face court-martial in more than a half-century.

But after two years of investigation and preparation, the prosecution is in disarray.

The Army’s lead trial counsel, Lt. Col. William Helixon, abruptly stepped down last month after confiding to superiors and the general’s defense team that he had qualms about the case. The Army scrambled to replace him, attributing his departure to “personal reasons” and saying in court papers that he was in “a state of extreme emotional distress.”

Meanwhile, the general’s lover-turned-accuser — an Army captain 17 years his junior — faces lingering questions about her credibility. Although she has testified that Sinclair twice forced her to perform oral sex against her will in Afghanistan, she has been unable to recall the exact dates and has given conflicting accounts to investigators and colleagues.

In January, more doubts surfaced when she testified at a pretrial hearing that she had stumbled across an old iPhone in her apartment that contained messages between her and Sinclair. Although she testified she had recently found the phone and that it hadn’t been turned on in years, experts for both the prosecution and defense said forensic evidence showed that the phone had been used several times late last year, raising questions about the veracity of her account. The Washington Post generally does not identify alleged sexual-assault victims.

Sinclair, a married paratrooper and former commander with the storied 82nd Airborne Division, is scheduled to return to the dock Tuesday in a small Fort Bragg courtroom. He has pleaded not guilty to all charges, although his attorneys have acknowledged that he had an affair with the captain. The Army has set aside most of the month for the court-martial.

The Army’s handling of the case is being watched closely in Washington, where the Senate is scheduled to soon consider a major bill that would strip military commanders of their long-standing authority to prosecute sexual assaults and other major crimes.

The bill, introduced by Sen. Kirsten Gillibrand (D-N.Y.), is a response to concerns that military commanders have systematically failed to deter and police sex abuse in the ranks. Gillibrand has said that a majority of senators favor her proposal, which would give uniformed prosecutors the power to decide whether to press charges. But it is unclear if she has enough votes to surmount procedural obstacles in the Senate.

Leaders at the Pentagon have lobbied fiercely against the bill, arguing that commanders need to retain legal authority to enforce order and discipline in their units. Both sides agree that the bill would represent the biggest changes to military law in decades.

The prosecution of Sinclair has been seen as a test case of the Army’s willingness to hold senior leaders accountable for sex crimes. With the Senate vote expected to be extremely close, any ripples from the Fort Bragg court-martial could easily influence the results.

“It’s really very unusual that you have a confluence of legislative and political processes like this at the same moment,” said Eugene R. Fidell, a lecturer in military law at Yale University. “It couldn’t be clearer that these are interactive and likely to reflect the other.”

The Fort Bragg case, however, has turned some common political arguments about sexual assault in the military upside down.

In the past, advocates for victims of sex crimes in the military have argued that commanders have been too quick to dismiss their accounts of rape and abuse and too reluctant to press charges against fellow officers.

Sinclair’s lawyers assert that the opposite is true in his case. They said the evidence against him is flimsy but that senior Army leaders are afraid they will be portrayed as covering up for one of their own if they drop the most serious charges.

“In a sense, I understand the fear that they have, and that it is driving their lack of doing the right thing, but that is not how the system is supposed to work,” said Richard L. Scheff, a civilian attorney who is representing Sinclair. “It’s supposed to be driven by evidence and by what is fair and just, not fear.”

In court filings, Scheff has said that Helixon, the former lead prosecutor, bluntly told him in a Feb. 9 telephone conversation that he had come to the conclusion that the sexual assault charges against the general should be dropped, but senior Army leaders had insisted the case go forward because of “politics and outside pressures.”

In an interview, Scheff said he was taken aback that a prosecutor would admit such a thing to a defense attorney. “Was I stunned? Yes, in bold, large font,” Scheff said. “He wanted to do the right thing. He’s got strong ethics and a strong moral compass.”

Helixon resigned from the case two days later. He did not respond to a request for comment placed through an Army spokesman.

In a court filing Friday, the Army acknowledged that Helixon had told his superiors that he thought the sexual assault charges against Sinclair should be dismissed for “tactical” reasons because they “would be difficult to win at trial.”

But in the military justice system, prosecutors don’t decide whether charges should be pursued or dropped. That’s up to senior commanders. And the Army made clear that it would proceed.

“There undeniably remain reasonable grounds to believe that the accused committed the sexual assault offenses,” the new prosecutor, Lt. Col. Robert Stelle, said in the court filing.