Story highlights Suit names academies' superintendents, Army, Navy and former DoD secretaries

Karley Marquet and Annie Kendzior both say they were raped at service academies

Both say they believed their cases were being investigated, but they weren't

Defense secretary announces new policies for sexual assault reports

Karley Marquet and Annie Kendzior said they enrolled at two of the nation's most prestigious military academies to serve their country and become military officers. Instead, they claim, they were raped -- and their military careers are now over.

In a lawsuit filed in U.S. Federal Court on Friday, the women claim the U.S. Military Academy in West Point, New York, and the U.S. Naval Academy in Annapolis, Maryland, ignored "rampant sexual harassment."

The suit claims former Secretary of Defense Robert Gates, the former superintendents of the two academies and the current secretaries of the Army and Navy are "personally responsible" for failing to "prevent rapes and sexual assaults at the Naval Academy and West Point."

Karley Marquet was a high school honor student, championship swimmer and all-star rugby player. She could have gone to college anywhere with her credentials, but Marquet chose West Point.

"When I was accepted, it was kind of overwhelming," she says. "You can't imagine having that structure and discipline but at the same time having people look at you like, 'Wow, you're doing something great for our country.'"

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But Marquet said her dream of becoming an officer was shattered in January 2011, her second semester at West Point.

Marquet said she got sick over a holiday weekend and stayed behind on campus. Her roommate was out of town and she was alone in her room.

It was then, Marquet, said, that an upperclassman she knew showed up at her door late one night to talk "girl troubles."

"I kind of felt cool that an upperclassman wanted to be friends with me and was seeking my advice," Marquet recalls.

After a drink, Marquet said, he persuaded her to go to his room.

"I just remember getting more and more intoxicated and my judgment really started to become impaired. ... I remember him turning off the lights and me asking, 'What are you doing?' And then he proceeded to rape me."

Marquet said she woke up disoriented, in physical pain, afraid to come forward.

"I was scared it was going to ruin my career," she said, "I was scared if I said anything, there would constantly be a target on my back."

According to the lawsuit, Marquet became depressed and suicidal "as a result of the rape and hostile environment" at West Point.

She filed a report and requested an investigation.

"The reason I ended up telling someone is because I didn't want that to happen to anyone else," Marquet said tearfully.

Karley Marquet became "depressed and suicidal" after the alleged incident and dropped out of West Point.

Annie Kendzior described herself as a "girly-girl" who never imagined she would end up in the military.

Kendzior was also an all-star student and one of the best high school soccer players in the country. She was recruited by Ivy League schools to play soccer, but she said the Naval Academy was more convincing.

"All of their graduates from the soccer team went on and became pilots and Marine officers," Kendzior said. "It just sounds like those women are so powerful and so well-respected, and I wanted to be that woman."

So in the fall of 2008, Kendzior headed off to Annapolis. She said her goal was to fly F-18s but it wasn't long after arriving at the academy she realized that wasn't going to happen.

"I could tell that there was a bias towards women," Kendzior recalled. "You're a female entering into a fraternity. A giant frat."

During one of he first weekends at the academy, Kendzior was invited to a party off campus. "I was like, 'OK, cool! College, finally! I can live the college life for one night."

But Kendzior said she had way too much to drink, so when a fellow midshipman offered her a place to crash, she accepted.

"I was like, 'OK, you know, it will be fine. I trust you. You're an upperclass," Kendzior remembers, "Because that's what they teach you, to trust your upperclass."

But Kendzior says that didn't happen. She was raped.

"At one point in the middle of the night, I did come to and he was on top of me," Kendzior said. "And I remember saying 'No,' but I just passed out again.

Kendzior said, she too, was afraid to come forward.

"I didn't want to be the girl that got the athlete kicked out, We had been told stories about how that happened in the past and I didn't want to be that next story."

For the next two years Kendzior said she battled depression and thoughts of suicide. It was a secret she couldn't keep anymore. When she told her father what happened, he encouraged her to file a report and request an investigation.

Marquet and Kendzior said they believed their cases were being investigated.

Marquet remembered investigators meeting with her parents about her case. "They promised my parents that if he wasn't going to jail, they could at least get him kicked out of West Point with the evidence they had," she said.

But both women said their alleged perpetrators were never punished and are still in the military.

Marquet and Kendzior are not alone. Reports of sexual assault at West Point, the Naval Academy and the Air Force Academy in Colorado Springs, Colorado, are up nearly 60 percent, and according to the Department of Defense, of the 65 reports investigated, only one resulted in a court-martial.

And it's that rise in reports of sexual assault that has the top man at the Pentagon, Secretary of Defense Leon Panetta, changing the rules.

"We've got to train commanders to understand that when these complaints are brought, they've got to do their damnedest to see that these people are brought to justice," Panetta told CNN's Kyra Phillips in an exclusive interview.

Panetta could not comment on Marquet's and Kendzior's cases specifically because of privacy issues, but he made clear that blaming of the victim needs to stop.

"I think that's part of the syndrome that we're dealing with, which is that once a decision is made that somehow this prosecution is not going to move forward then you basically turn on the victim who brought that complaint," Panetta said. "That syndrome is what we have to break out of."

Just last week, after the CNN interview, Panetta announced he has created a Special Victims Unit to investigate sexual assault allegations, and that sexual assault allegations will be dealt with at the level of colonel instead of slowly making their way up through the chain of command.

But the changes in policy have come too late for Karley Marquet and Annie Kendzior. Their military careers are over.

According to the lawsuit, "as a result of the rape," Marquet became "depressed and suicidal." She said she was unable to handle the stress of seeing the alleged perpetrator every day, so she resigned from West Point.

Kendzior said she also became suicidal. She was diagnosed with borderline personality disorder and according to her lawsuit, was then "forced to leave the academy."

The two women said they are telling their stories so that others at the academies will feel comfortable coming forward.

"I know that with at least one person coming forward there will be others who want to come forward and say something," Marquet said.

Similarly, Kendzior said, "I want to encourage other women to report as soon as possible because then they might get their perpetrators put behind bars, which is where they should be, which is where they deserve to be."

West Point and the Naval Academy told CNN they were unable to comment on the allegations due to privacy issues. Both women have requested copies of their case files to learn more about why their alleged perpetrators are still in the military.