>> the dungeon. >> these research chimps are getting their first taste of freedom. but what about the unlucky ones still behind bars? the last season. at 39 he's banking his career on a risky experiment. >> i'm laying in bed and thinking am i delusional? >> one man's willingness to do anything for one last chance to play a sport he can't live without. revealing investigations. fascinating characters. stories with impact. this is "cnn presents" with tonight's hosts, randi kaye and drew griffin. secretary of defense leon panetta announced new aggressive policies to combat sexual assault in the military. zero tolerance is the message from the pentagon's top commander. >> but ground zero for battling the growing problem may start at the nation's most prestigious military academies. >> reports of sexual assaults at the academies rose by nearly 60% in the past year. and out of the 65 cases reported only one resulted in court-martial. >> that is why two young women say they're coming forward. in a lawsuit just filed they allege they were raped in their first year at the academies. tonight they speak to kyra phillips for the first time. >> reporter: west point, the naval academy, the air force academy. prestigious military institutions tasked with training future officers ethically, spiritually, and morally. but for these high school honor students their experience would be far different. >> i remember him turning off the lights and me asking what are you doing? >> in the middle of the night i did come to, and he was on top of me. >> karley marquet and annie ken kendsior say they were raped. raped by fellow classmates they trusted and ignored by a chain of command that promised their parents they'd be protected. >> and nobody, not a single person, not one, was looking out for her best interest. >> come on, karley. >> reporter: karley marquet was not your typical teenage girl. that's her cage fighting at 18. >> that's it, karley. >> reporter: an all-star rugby player. a championship swimmer and honors student. karley could have gone to college anywhere. what was it about west point that drew you to that academy? >> just knowing you kind of have your future set, 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. >> reporter: her sister was a mid-shipman at the naval academy, her father a marine. to karley they were heroes. everything she wanted to be. do you think west point let you down? >> yeah. i wanted to be there. it was my dream. >> reporter: a dream that was shattered her first year, when an upper classman showed up at her door to talk girl troubles. >> i kind of felt a little cool that an upper classman wanted to be friends with me and was seeking my advice. >> reporter: after sharing a drink karley says he convinced her to come to his room. since he was an upper classman she trusted him. >> i remember just 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. >> reporter: karley says she woke up disoriented, in physical pain, and afraid to come forward. >> i was scared it was going to ruin my career. i was scared if i said anything that there would constantly be a target on my back. i reached out to people, and they weren't there. i just didn't want to leave my room. i mean, he was right across the hall. >> and you still had to work under him, take out his trash. >> yes. >> why? >> it was part of our duties. >> chain of command? >> mm-hmm. >> reporter: chain of command. military ranks where senior students have authority over the one immediately below. so every day karley had to face the man she says raped her. but weeks later karley finally found the courage to come forward. she filed a report and asked an investigation. >> and the reason i ended up telling someone is because i didn't want that to happen to anyone else. >> reporter: annie kendzior describes her as a girly girl who never imagined joining the military. an honor student and one of the best high school soccer players in the country, she was heavily recruited by top ivy league schools. but the naval academy was the most convincing. >> all their graduates that graduated from the soccer team went on and became pilots and marine officers. and it just sounded like oh, those women are so powerful and so well respected, and i wanted to be that woman. >> reporter: annie's goal was to fly f-18s. but it wasn't long after arriving she realized that wasn't going to happen. >> i could tell that there was definitely a bias toward the women. i mean, you're a female entering into a fraternity, a giant frat. >> reporter: annie says there were no derogatory names for the men but for the women they were called dubs. >> what does dub mean? >> dub, a dumb ugly bitch. >> were you ever called a dub? >> every girl was called a dub. >> reporter: it was definitely a different culture, and annie felt out of place. so when she got invited to go to an off-campus party, she was in. >> i was like okay, cool. college, finally. i can live the college life for one night. >> reporter: but annie says she had way too much to drink. so when a fellow midshipman offered her a place to crash, she accepted. >> i was like, okay. it'll be fine. i trust you. you're in upper class. because that's what they teach you to trust, your upper class. >> so tell me what happened once he took you back to the room. >> i just laid down and went to sleep. at one part in the middle of the night i did come to, and he was on top of me. and i remember saying no. but then i just passed back out again. >> reporter: annie was afraid to come forward. >> why were you scared? >> i didn't want to be the girl that got the athlete kicked out. because we had been told stories about how that had happened in the past. and i didn't want to be that next story. >> reporter: for two years annie battled depression and thoughts of suicide. she had a secret she couldn't keep anymore. and finally called her father. >> and she said, "i was raped." and i couldn't breathe. >> reporter: still ahead, the battle to change the system. >> how do you get it through these men's heads if they rape they will pay the price? 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[ male announcer ] while others are content to imitate, we'll continue to innovate. the lexus rx. why settle for a copy when you can own the original? see your lexus dealer. in a lawsuit just filed allegations of rape at west point and the naval academy, two young women say they risked their careers to come forward and request an investigation. they wanted the men they say raped them to be prosecuted. one year later they're still waiting. kyra phillips continues our investigation. >> reporter: when karley marquet came forward to say she was raped at west point, she believed her case would be investigated. >> i remember the investigators meeting with my parents, and 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. >> but he's still there. >> but he's still there. >> reporter: annie kendzior says she too believed her allegations of rape would be investigated. >> i was like, okay, they're going to get him. like, good. >> reporter: but karley and annie say their alleged perpetrators were never punished. so now they've filed a lawsuit, naming former secretary of defense robert gates, the former superintendents of west point and the naval academy, secretary of the navy ray maybis, and secretary of the army john mchugh. the lawsuit claims there was limited support from commanders and failure to ensure sexual predators were prosecuted and incarcerated for their crimes. karley and annie are not alone. reports of sexual assault at the academies are up nearly 60%. and of the 65 reports investigated last year, only one resulted in a court-martial. >> i ache for those former cadet midshipmen who have had their lives torn up. it shouldn't be that way. >> reporter: congresswoman jackie speier has gone to the house floor 19 times. >> we need to overhaul this system. >> reporter: demanding that congress and the military change the way sexual assaults are prosecuted. >> you report everything through your chain of command. so i'm raped, i go to my commander, i say i've been raped. my commander can say to me, well, you know, i'm not going to pursue this. or take an aspirin and go to bed. as long as it's going to be in the chain of command, there's always going to be a conflict. >> reporter: her bill, the stop act, would take investigations away from the chain of command and turn them over to an impartial council of civilian and military experts. >> if you're not going to have your assailant prosecuted, why would you want to come forward? because you're basically setting yourself up to lose your career in the military. >> reporter: speier says for years her calls to action have gone unanswered until secretary of defense leon panetta took office. >> we've got to train commanders to understand that when these complaints are brought they've got to do their damnedest to make sure these people are brought to justice. that's the only way we're going to try to prevent this in the future, is to show that people can't get away with it. >> how do you get it through these men's heads if they rape they will pay the price? >> this place operates by command authority, and it has to begin at the top, and the message has to go down to the bottom. >> reporter: still, panetta will not take investigations away from the chain of command. but he is changing the rules, announcing new initiatives just one week after our interview. >> what i will do is change these cases are hanltd handled military. >> reporter: here's what panetta is doing differently. he created a special victims unit to investigate sexual assaults. now instead of slowly making their way up the chain of command all cases will begin at the level of colonel. >> everybody has to do due diligence. commanders, like i said, have bosses. if that commander's not doing their job, you relieve their butts of command. >> reporter: major general mary kay hertog heads the sexual assault response and prevention office. >> you have to look at this every single day and you have to look at what every victim says seriously. i want our victims to come forward. >> reporter: but the changes in policy come too late for karley marquet and annie kendzior. their military careers are over. >> it hurts me to hear that because we betrayed their trust and we didn't take care of them and we need to do a much better job. >> reporter: according to the lawsuit, as a result of the rape karley became depressed and suicidal, unable to handle the stress of seeing her alleged perpetrator every day. karley resigned from west point. >> i felt like a blemish. >> because they knew you reported the rape. >> mm-hmm. >> reporter: annie says she too became suicidal. she was diagnosed with borderline personality disorder. and according to her lawsuit was then forced to leave the academy. >> it hurts the message that we're trying to get out there, that -- >> reporter: because of privacy issues panetta couldn't comment specifically on karley and annie's cases. but he does make clear that blaming the victim needs to stop. >> personality disorder. academic separation. i mean -- >> i think that's part of the syndrome that we're dealing with, which is that, you know, 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 and try to do everything possible to make sure that that victim doesn't hang around or really diminish them by somehow accusing them of having psychological problems. that syndrome is what we have to break out of. >> reporter: and for karley and annie if coming forward helps with that mission they want to be a part of the battle. >> i know with at least one person coming forward there will be others that want to come forward and say something. >> because then they might get their perpetrators put behind bars, which is where they should be. >> west point and the naval academy say they couldn't comment on karley and annie's allegations because of privacy issues. both women have requested copies of their case files to learn more about why the men they say raped them are still in the military. coming up -- from the laboratory to freedom. the journey of a group of chimps that get a new lease on life. 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(female announcer) most life insurance companies look at you and just see a policy. at aviva, we do things differently. we're bringing humanity back to life insurance. that's why only aviva rewards you with savings for getting a check-up. it's our wellness for life program, with online access to mayo clinic. see the difference at avivausa.com. the disney film "chimpanzee" just out this week shows the cute creatures enjoying life in the wild, acting a lot like us. but thousands of chimps being used for research here in the united states are cooped up in cages. there's a fierce debate over whether the primates should be forced to endure that kind of captivity. a bill before congress would ban invasive research on chimpanzees. john zarrella follows a group of chimps whose research days are finally over and looks at what's ahead for those who aren't so lucky. >> reporter: winter snow came early. melting now under a warming december sun. a new season begins, and for some the beginning of a cross-country journey. to freedom. you hear them long before you see them. when you see them, their features are unmistakable. ten chimpanzees are here, with names like bart and sarah. >> sarah, you want to play? no. bart wants to hog all the attention. >> reporter: they've lived most of their lives behind these walls. some for decades. they were research chimps used to test everything from the toxicity of pesticides in hairsprays to cures for aids and hepatitis. now these are the last of 266 to leave this one-time biomedical lab, the colston foundation, in alamogordo, new mexico. for jen firestein, sanctuary director of the save the chimps foundation, it is a promise fulfilled. >> failure was never an option for us. and the only thing that's ever slowed us down is that it takes a long time for the chimps to get used to living in family groups because they didn't have that opportunity growing up. >> because this is where they lived. >> reporter: exa >> exactly. >> reporter: firestein is finishing a dreem begun by her late boss carol noon to give these animals who had had blood draush drawn and biopsied a life where they can be quite simply chimps. a decade ago frederick colston lost federal funding after numerous violations of the animal welfare act. in one case three chimps literally cooked to death when their enclosure heated to 140 degrees. colston, now deceased, denied abuse accusations during a 1995 interview with cnn. >> we don't abuse animals. we try to treat them according to the regulations and the law and even beyond that. >> reporter: facing bankruptcy, he finally sold the facility and animals to save the chimps. it was the beginning of a great migration. for ten years a dozen or so at a time have left the cold walls and steel bars for a new home, an island sanctuary. >> this is the last crew. >> the last crew. >> this is the crazy young wonderful vivacious crew. >> well, they're kind of mellowed right now -- >> reporter: veterinarian jocelyn bessner checks her charges. >> what i want to do now is just go over each one, make sure they look healthy. >> reporter: bart was born here. he turned 20 on january 14th. like most of the chimps his records are sketchy at best. >> so we don't know what the study was for. we just know that he was in a study. >> reporter: experts say every chimp has its own personality. bart's is spitting vinegar. he interrupts my conversation with besner. >> that's the testosterone. >> reporter: he was getting a kick -- >> oh. >> reporter: -- out of his antics. the concrete and steel enclosures have been modified with pass-throughs. the chimps can visit each other, play, roughhouse. it wasn't that way before save the chimps took over. >> so this is the infamous -- >> this is the dungeon. >> the dungeon. >> this is the dungeon. and this is a small cage that they lived in. >> wow. >> reporter: like a prison, one cell after another. chimps lived this way, sitting day after day, year after year, until needed for a research project. >> what do you feel like when you walk in here? >> it's almost like it's haunted. it's a really dismal place. there's not really a lot of good memories here for any of us. >> reporter: here at least it's just memories. the story is much different a few miles down the road at holoman air force base. before humans flew in space, a chimp named ham did. not that he had a choice. the old footage shows chimps being trained, examined, playing, and dying. a chimp strapped into a form-fitting shell is secured inside a cylinder on a rocket sled. he's propelled down the track to test survivability after a sudden stop. the answer is evident in the lifeless body. once no longer needed, most of these air force chimps eventually ended up in the hands of, you guessed it, frederick colston. by the mid '90s colston ran two facilities just miles apart. a rare air force tour in 1997 shed light on the research they were subjected to under colston. >> that animal was -- has been inoculated with hiv. it's on hiv protocols. >> reporter: the chimps are now owned by the national institute