A three-star Air Force general whose handling of sexual-assault cases drew withering criticism from advocacy groups and some lawmakers retired under pressure Wednesday.

Lt. Gen. Craig Franklin, the commander of the Third Air Force in Europe, acknowledged that he had become a “distraction” for the Air Force because of controversial cases in which he overturned a sexual-assault conviction of a star fighter pilot and decided that there was not enough evidence to court-martial an accused rapist.

In a statement, Franklin said he was retiring “for the good of this command and the Air Force” because of persistent doubts about his impartiality in overseeing sex-abuse investigations.

“Public scrutiny will likely occur on every subsequent case I deal with,” Franklin said. “The last thing I want in this command is for people to feel they cannot bring a sexual assault case forward or feel like it won’t be dealt with fairly.”

Franklin’s decision to grant clemency in February to a convicted fighter pilot at Aviano Air Base in Italy helped spark a national debate over sexual assault in the armed forces and about whether military leaders took the problem seriously enough.

The pilot, Lt. Col. James Wilkerson, had been found guilty in November 2012 by an all-male jury in what was seen as a test of the Air Force’s willingness to tackle such crimes. Franklin’s decision to grant clemency infuriated many female lawmakers and activists, who said the outcome would discourage victims from reporting abuse.

Congress has since passed several measures to bolster the investigation of sex crimes in the military and has stripped commanders of the authority to overturn convictions — an outcome of Franklin’s decision in the Aviano case.

But some lawmakers had continued to press the Air Force leadership to take action against Franklin, particularly after the Air Force took the rare step last month of reopening a sexual-
assault case
that the general had closed for lack of evidence.

In an interview, Sen. Claire McCaskill (D-Mo.), who had repeatedly urged the Air Force to remove Franklin from command, said he had created an atmosphere in which, “no matter how you look at it, victims could not feel completely comfortable with reporting these crimes.”

Franklin initially gave no reason for granting clemency in the Wilkerson case. But after his decision received widespread media coverage, he released a six-page letter to defend himself.

He explained that after reviewing the case file, he had nagging doubts about the victim’s credibility. He also said he had a hard time believing that the accused pilot could have committed “the egregious crime of sexually assaulting a sleeping woman,” given that he was “a doting father and husband” who had been selected for promotion.

The letter only made things worse for Franklin politically and helped persuade some members of Congress to curtail the authority of commanders to intervene in such cases.

In addition, Franklin’s description of the pilot as a model husband was undercut when another woman accused Wilkerson of committing adultery and fathering a child out of wedlock years earlier. The Air Force confirmed the allegation and forced Wilkerson to retire.

“Military leadership supported Franklin for far too long,” said Nancy Parrish, president of Protect Our Defenders, an advocacy group that represents sex-crime victims. “While he should have been removed a year ago, it is good to hear that they finally have done the right thing.”

Franklin is scheduled to step down Jan. 31 as Third Air Force commander. Air Force officials said that he was not forced to retire, but they acknowledged that he had been under scrutiny.

“I fully respect his decision and the difficult circumstances under which he made it,” Gen. Mark Welsh, the Air Force chief of staff, said in a statement.