Army Brigadier General Jeffrey Sinclair leaves the courthouse at Fort Bragg in Fayetteville, North Carolina. REUTERS/Ellen Ozier/Files

Fort Bragg, North Carolina - A US Army general at the center of a rare court-martial of a top military leader was cleared of sexual assault charges on Monday, but admitted to mistreating a junior officer during their inappropriate sexual relationship.

Brigadier General Jeffrey Sinclair pleaded guilty to several lesser military criminal offenses as part of an agreement with the government that dismissed the most serious allegations against him.

The 27-year Army veteran said he knew the female Army captain with whom he had a three-year extramarital affair was enamored by his rank, and he led her on despite knowing he would never divorce his wife.

When he realized his subordinate was emotionally committed to the affair in a way he was not, he flirted with other women and was cold to her in hopes she would become angry enough to break off their secret liaison that spanned two war zones, Sinclair told a judge.

“I failed her as a leader and as a mentor and caused her harm to her emotional state,” the one-star general said.

Though vindicated of charges that he forced the captain to perform oral sex and engaged in “open and notorious sexual acts” with her, Sinclair's decorated military career is almost certainly over.

Sinclair's attorneys will argue during the sentencing phase on Monday that he should avoid jail time and be allowed to retire at a reduced rank in keeping with how officers in similar cases have been treated.

The lawyers say Sinclair's case is one of the first courts-martial of a general in nearly 60 years and was fueled by political concerns at a time when the US military is grappling with how to handle rising sexual assault in its ranks.

“Clearly what General Sinclair did was wrong, but it certainly had the appearance that he was being the scapegoat for the bigger sexual assault problem that the military's going through,” said Morris Davis, a retired Air Force colonel and former chief prosecutor for terrorism trials at Guantanamo Bay, Cuba, who is not involved in the case.

Sinclair, a 51-year-old married father of two, has remained on active duty at the sprawling base at Fort Bragg after being stripped of command in southern Afghanistan in May 2012 as a result of the criminal allegations.

His trial was already under way this month when a judge ruled that politics appeared to have improperly influenced the Army's decision to reject an earlier offer by Sinclair to plead guilty if the charges of coercive sex acts were dropped.

The former lead prosecutor in the case resigned after military leaders refused to dismiss the sex charges despite concerns about the key accuser's credibility. The new chief prosecutor said the government did not doubt the woman's underlying allegations.

The judge last week allowed Sinclair to renew his plea offer, and the general's attorneys announced on Sunday that a resolution to the case had been reached.

The agreement called for the government to drop the sexual assault charges involving the captain, as well as two additional charges that could have required Sinclair to register as a sex offender.

The identity of the captain, a military intelligence officer, is being withheld by Reuters due to the nature of the charges.

Sinclair pleaded guilty to maltreating his accuser, using his government credit card for personal purposes related to the affair and using demeaning language to refer to female staff officers.

He admitted to calling a female major “a red-headed troll” but told the judge he was joking when he said “I'm a general, I'll say whatever the fuck I want.”

Sinclair also faces punishment after pleading guilty this month to having an adulterous affair, asking junior female officers for nude photos and possessing pornography on his laptop while deployed in Afghanistan.

He could have been sent to prison for life if he had been convicted of the sexual assault charges, but now faces a far less severe maximum sentence.