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Ms. Messick was unable to move, cry or scream. She was a 19-year-old from rural Florida, in her fifth week of basic training at Lackland Air Force Base, and she had just been assaulted by the man the Air Force had entrusted with her life.

After the April 2011 attack, Ms. Messick completed basic training, following orders from the instructor for nearly a month more. Afraid of the consequences, she did not tell anyone what he had done. "How am I supposed to go about reporting something," asked Ms. Messick, "when the person I'm supposed to report to is the person who raped me?"

Now, after leaving the Air Force, Ms. Messick is the first victim of a still-unfolding sexual assault scandal at Lackland to speak publicly about what she has endured. Since accounts of sexual violence at the base began to surface in late 2011, it has emerged as the largest such episode in Air Force history.

Ms. Messick, now 21, is one of 62 trainees identified as victims of assault or other improper conduct by 32 training instructors between 2009 and 2012 at Lackland, a sprawling base outside San Antonio that serves as the Air Force's basic training center for enlisted personnel. So far, seven Air Force instructors have been court-martialed, including Staff Sgt. Luis Walker, now serving a 20-year sentence for crimes involving 10 women, including Ms. Messick. Eight more court-martial cases are pending. Fifteen other instructors are under investigation, and two senior officers have been relieved of command.

While Air Force officials say they have taken steps to better protect their most vulnerable personnel, including appointing a female commander to oversee basic training and tightening supervision of instructors, critics say they do not go far enough in addressing an issue across the military: a high rate of sexual assaults that are often not reported because women fear reprisals. None of the victims at Lackland told Air Force officials of the attacks, and the episodes came to light only when a female trainee who had not been assaulted disclosed what she knew.

The reforms undertaken by the Air Force do not alter a fundamental fact of military life: commanders have final say over whether criminal charges are brought in military courts, and victims are expected to report crimes to those who oversee their careers.

In response to the growing outcry over sexual violence, the Pentagon last year ordered that charging decisions in sexual assault cases be determined by more senior commanders than in the past, but the directive stopped short of taking the decision out of the chain of command. Some other nations, including Britain, have taken steps to create a more independent military judicial system, but experts on military justice said that the United States has been unwilling to do so.

"The military justice system is not only to judge innocence or guilt, but is also designed to help a commander ensure good order and discipline," said Dwight Sullivan, an appellate defense counsel for the Air Force. "Those things sometimes come into conflict."

While more than 3,000 sexual assault cases were reported in 2011 throughout the military services, Leon E. Panetta, the departing defense secretary, has said the real figure could be as high as 19,000. The Defense Department has found that about one in three military women has been sexually assaulted, a rate twice as high as that among civilians.

"It's no mystery why they don't come forward," said Laurie Leitch, a psychologist who deals with assault cases in the military. "It is like going to your boss to report that you have been sexually assaulted. How realistic is that?"

Air Force commanders say they have taken preventive action at Lackland. "There wasn't much supervision," said Maj. Gen. Leonard A. Patrick, who is in charge of the Air Force's enlisted training. "But now we want to put more leadership into the equation, and more accountability."

Several female recruits said in recent interviews that they feel safe under the new system, in which instructors no longer have sole oversight for a group of trainees and a buddy system has been instituted. "The scandal was kind of in my mind when I signed up, but I haven't had any problems," said Chanler May, a 19-year-old from Texas.

But Ms. Messick is skeptical. "It's not like anything has really changed," she said in an interview.

Identified by the news media during her assailant's court-martial only as "Airman 7," Ms. Messick suffers from post-traumatic stress disorder. She said she decided to speak out because she believes doing so will be therapeutic, and she hopes to help change how the military deals with victims of sex-related crimes. "I don't want anyone else to go through this," she said.

When she joined the Air Force in March 2011, Ms. Messick was excited to leave her hometown, Baker, Fla. She was assigned to an all-female "flight" — a training group — overseen by Sergeant Walker. About 25 percent of those in basic training are women; the Air Force has the highest proportion, 19 percent, of women on active duty in any of the services, Pentagon statistics show.

Ms. Messick recalled that her group rarely saw any supervisor other than Sergeant Walker. He quickly began to single her out for special treatment.

He repeatedly allowed her to use his office computer to check her e-mail, a violation of basic training rules. On one office visit, Sergeant Walker grabbed her and began to grope her, Ms. Messick said. She demanded that he stop. "He said, 'I swear it won't happen again,' " she recalled.

But not long after that, Sergeant Walker ordered Ms. Messick to deliver towels to an empty floor in the trainee dorm. There, she said, he raped her.

Afterward, Ms. Messick tried to cope in silence. In May 2011, only a month after the assault, she impulsively married a friend in the Air Force. "I think I was trying to find some kind of protection," she said. They divorced just months later.

But later that year, while she was in an advanced training program in Mississippi, a friend from basic training contacted her, reporting that Sergeant Walker was sending explicit photos of himself and demanding that she do the same. In the process, he had threatened to ruin Ms. Messick's military career. Ms. Messick said she told her friend that the two had had sex, but did not describe it as rape. When Air Force investigators looking into the instructor's conduct tracked down the friend, she told them about Ms. Messick.

After two and a half hours of questioning by the investigators, Ms. Messick said she provided a "watered down" version of the episode with Sergeant Walker — acknowledging they had sex but refusing to offer details. "I was scared to death. And I kind of blocked out what happened," she said. "It took me a long time to say the word 'rape.' "

But in testifying at Sergeant Walker's court-martial in 2012, she recalled, she faced the instructor and accused him of raping her. Lt. Col. Mark Hoover, an Air Force lawyer involved with the Lackland prosecutions, does not dispute Ms. Messick's account. But because she had not disclosed the rape in pretrial interviews, Sergeant Walker was only charged in her case with a lesser count of engaging in an unprofessional relationship involving sodomy and sexual intercourse.

In July 2012, he was convicted on 28 counts, including rape, sexual assault and aggravated sexual contact involving 10 trainees. Joseph A. Esparza, one of Sergeant Walker's lawyers, declined to comment, saying that his case is on appeal.

After the court-martial, Ms. Messick said she felt lost. Out of the Air Force because of an injury, she went back home to Florida, but her PTSD grew worse. One day she smashed a vase and used the broken shards to slice her hands. "I just wanted to stop hurting," she said.

Her mother, Marla Simmons, called the Air Force lawyer who had dealt with her daughter. "I was really upset and I told him he had to get her some help, right now, or somebody is going to pay for what they have done to her," she said.

The lawyer arranged for Ms. Messick to get into a therapy program at a nearby Department of Veterans Affairs hospital, which she said helped. Last December she remarried.

Still, she said that her PTSD often paralyzes her. She added that other Lackland victims are also suffering from the disorder. "There are some women who can't say what happened to them," she said. "They have nightmares. It takes over your life."

Today, she laments that the military experience she had dreamed would change her life has turned out to be such a bitter one.

"They are not doing anything for the people who have been through it," she said of the Air Force's treatment of the assault victims. "They haven't come to me or any of the other girls to ask them what to change. They basically have left me to fend for myself."

Thursday: Female veterans in limbo.