"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.