FORT BRAGG, N.C. — The sexual assault case against an Army general was thrown into jeopardy Monday when the judge said the military may have improperly pressed ahead with a trial to send a message about its determination to curb rape and other widespread misconduct.

Judge Col. James Pohl refused to dismiss the charges against Brig. Gen. Jeffrey A. Sinclair but offered the defense another chance to plea-bargain the case with a set of military officials not previously involved with the matter.

The twist comes with the Pentagon under heavy pressure from Congress and beyond to combat rape and other sex crimes in the military. Late Monday, the Senate unanimously approved a bill making big changes in the military justice system to deal with sexual assault.

The judge reviewed newly disclosed emails in Sinclair’s case and said he found the appearance of “unlawful command influence” in Fort Bragg officials’ decision to reject a plea bargain with the general in January.

Under the military code of justice, the decision was supposed to be decided solely on the evidence, not its broader political implications.

Pohl said the emails showed that the military officials who rejected the plea bargain had discussed a letter from the accuser’s lawyer. The letter warned that allowing the general to avoid trial would “send the wrong signal.”

Sinclair’s attorneys have until Tuesday morning to decide whether to submit a plea-bargain proposal again or proceed with the court-martial, which began last week.

Sinclair, the 51-year-old former deputy commander of the 82nd Airborne Division, is accused of twice forcing a female captain to perform oral sex on him in Afghanistan in 2011 during a three-year extramarital affair. He has admitted to the affair but denied assaulting the woman.

He is believed to be the highest-ranking U.S. military officer ever court-martialed on sexual assault charges. He could get life in prison if convicted.

The defense has portrayed the woman as a liar who concocted the allegations after she saw emails between Sinclair and another woman.

Richard Scheff, the general’s lead defense lawyer, said the defense has not yet decided what to do.

However, he said the new developments vindicate what the defense has been claiming for months — that the Army pressed ahead with a weak case for fear of the political blowback that would result from dropping charges against such a high-profile defendant.

“This is an unprecedented situation. It’s a mess created by the government. It wasn’t created by us. We have so many options, we don’t even know what they all are,” Scheff said.

Lt. Col. Robert Stelle, the lead prosecutor, declined to comment after the hearing.

In December, Sinclair had offered to plead guilty to some of the lesser charges in exchange for the Army dropping the sexual assault charges, but he was turned down. His plea offer was discussed in emails among a high-ranking Washington-based Army lawyer, the prosecutors and the commanding general overseeing the case.

The judge said he doesn’t believe the whole case was tainted, just the decision on a plea agreement. He also criticized prosecutors for not giving defense lawyers the emails sooner: “The only reason we are in this conundrum is because of the government’s late notice.”

Meanwhile, the Senate approved 97-0 a military-justice bill that would scrap the nearly century-old use of the “good soldier defense” to raise doubts that a crime has been committed. Currently, those accused of wrongdoing can cite their good military records.

The Pentagon has estimated that as many as 26,000 military members may have been sexually assaulted in 2012, based on an anonymous survey.

Many victims are unwilling to come forward despite new measures to curb abuse, the military says.

Last week, Sinclair pleaded guilty to three lesser charges involving adultery with the captain and improper relationships with two other female Army officers. Those charges could bring 15 years in prison. A trial then began on the remaining sexual assault charges.

Now, in light of the judge’s ruling, the defense could ask to withdraw Sinclair’s guilty plea to those lesser charges.

In December, Sinclair’s accuser came out against a plea bargain on the more serious sexual assault charges in a letter sent by her attorney, Capt. Cassie L. Fowler. Fowler suggested that the proposed deal 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.

Though prosecutors deny any consideration was given to Fowler’s comments about the potential fallout, the emails turned over to the defense Saturday show they did discuss her assertions. One top military lawyer at Fort Bragg quoted her letter and said he found Fowler “very preachy.” It was Lt. Gen. James Anderson, as commander of Fort Bragg, who made the final decision on whether to accept Sinclair’s plea offer.

Testifying from Afghanistan by telephone, Anderson said he didn’t thoroughly read Fowler’s letter. The only thing he weighed in rejecting the deal was that the accuser wanted her day in court, he said.

But Anderson’s testimony appeared to be contradicted by a Dec. 20 email he sent to a military lawyer. “I have read the letter and made my decision,” Anderson wrote.

Scheff, Sinclair’s chief lawyer, told the judge Monday that the Army had been stonewalling him for months for evidence about those discussions.

“Every time we asked for these, the government has said we were going on a fishing expedition,” Scheff said. “And each time, we catch fish.”

Fowler said Monday that the courtroom maneuvering over her letter was “nothing more than an attempt to take the focus off the general’s gross misconduct.”

Associated Press writer Jeffrey Collins in Columbia, S.C., contributed to this report.