On Monday, the United States Army dropped sexual assault charges against Brigadier General Jeffrey Sinclair in exchange for pleading guilty to lesser charges. Sinclair is the highest-ranking officer in the US to be court-martialed on sexual assault accusations.

While the original charges could have led to life imprisonment, the plea deal is expected to result in a reduced rank for the general and a short prison sentence. The plea bargain comes several weeks after the US Senate killed a bill that would have allowed military prosecutors, not the commanding officers of accused offenders, to bring sexual abuse charges.

General Sinclair was accused of raping a female captain under his command multiple times and preventing this captain from leaving his unit. He was also accused of threatening to kill her, and her family, if she told anyone, as well as a host of other crimes.

Accepting the plea bargain in military court Monday, Sinclair admitted he had had a three-year sexual relationship with the captain, pressured soldiers under his command to text him nude photos of themselves, possessed pornography on his computer, disobeyed orders to stop the affair, and misused army credit cards for sexual visits. In his declaration of guilt, Sinclair stated that he had “failed her as a leader and as a mentor and caused harm to her emotional state.”

However, these relatively small crimes stand in sharp contrast to the testimony of the unnamed accuser. The captain broke down in tears in a seven-hour testimony on March 6 as she recounted being forced to perform oral sex on the general. “He grabbed me by the back of the neck and pushed me down. I tried to pull back, and he put his other hand on my shoulder … It felt disgusting. It felt like I had no control over my body.”

Later, she described a scene in which she suggested to the general that she would like to meet his wife. “He told me that if I ever told her or anyone else about he and I, he would kill me and then he would kill my family… and he would do it in a way no one would ever know.”

The captain’s attorney, Jamie Barnett, a retired rear admiral, told the Associated Press that Sinclair “ literally sabotaged her career by altering her orders to keep her under his command and refusing her many requests to be transferred. She was literally trapped and bullied by one of the highest ranking officers in the United States Army . ”

The case, like all court-martial cases, is presided over by an army judge and five army jurors who are all superiors to the accused. This case, however, took an unexpected turn when the judge, Colonel James L. Pohl, put a stop to the trial, arguing that a previous decision to go ahead with trial, rather than accept a plea bargain, was politically motivated.

One of the five military jurors, Lt. Gen. Joseph Anderson, had refused to accept a plea bargain that his compatriots wished to offer General Sinclair earlier this year. Judge Pohl argued that a letter sent to Anderson exerted undue influence on this decision, politically tainting the proceedings.

Capt. Cassie Fowler, an advocate of the accuser, had written to Lt. Gen. Anderson that accepting a plea “would only strengthen the arguments of those individuals that believe the prosecution of sexual assault should be taken away from the Army... (It) would send the wrong signal to those senior commanders who would prey on their subordinates.” Although Anderson testified he was in no way influenced by the letter sent to him, the case was halted and the jurors were sent back to their posts. Then, the defense lawyers were given a second chance to submit their plea bargain, this time to be reviewed by a commander other than Anderson. Eugene Fidell, a professor of military justice at Yale, told the New York Times that this change in events could “give the Army potentially a graceful way out.”

Under this plea deal Sinclair will avoid serious punishment. While the charges that Sinclair has admitted to could leave him in prison for 25-and-a-half years, according to the Times, “ the actual sentence is expected to be only a fraction of that.”

The military is hostile to even the slightest breach to their chain of command. Before the case against Sinclair began, the Senate struck down a bill that would have taken the decision to prosecute sexual assault cases out of the hands of the senior officers of the accused and put them into the hands of independent military prosecutors.

At the time, Senator Lindsey Graham (Republican) threatened that any senator hoping to run for president would ruin his or her chances by voting for the law. Chairman of the Senate Armed Services Committee, Senator Carl Levin (Democrat), opposed the bill, claiming there would be more sexual abuse “if we undermine the authority of the very commanders who must be at the heart of the solution.”

Sexual abuse is rampant in the military. The 2010 Department of Defense Annual Report on Sexual Assault in the Military states that in 2010, 108,121 veterans screened positive for some form of sexual trauma they were victims of during active military service.

Last year, 3,553 sexual assault cases were reported in the military; however, due to threat of demotion and other forms of intimidation, this reported amount is expected to be only a tenth of the actual yearly cases

In February, 588 soldiers were removed from posts as recruiters and sexual assault response coordinators after internal reports emerged implicating these soldiers in sexual assault and alcohol abuse.

Recently Stars and Stripes reported that Lt. Col. Joseph Morse, an army lawyer whose job is to train military lawyers handling sexual and physical abuse cases, is being investigated for alleged sexual molestation of a female Army lawyer at a training conference.