The young Coast Guard officer was often seen crying.

She had entered the US Coast Guard Academy with dreams of traveling the world, drawn to the agency's missions of protecting the environment and saving lives. But her emotional displays following her academy graduation in 1998 prompted one superior officer to question whether she was suicidal. He noted his observations in her personnel file, she says, resulting in a negative evaluation that tarnished her career.

Then, in September 2014, after being denied yet another a promotion, she said couldn't help but tell a colleague what she says had been troubling her for so long: She had been raped more than a decade earlier by an upperclassman at the academy, but leaders there had failed to investigate.

For years, as she silently struggled with the trauma of the attack, she was unable to advance in her career. Meanwhile, the man she said assaulted her saw his military career flourish.

After hearing the woman's allegations, the colleague felt required to report them, launching what would become the US Coast Guard's most sweeping investigation into sexual assaults at its academy. It exposed a disturbing history of rapes, assaults and other misconduct being ignored -- and at times -- covered up.

The damning results of the probe, dubbed Operation Fouled Anchor, were kept secret for years until CNN, which had gained access to the findings, questioned the agency about its handling of the investigation. Those questions prompted the Coast Guard to brief Congress in recent weeks. Until then, the document was "very centrally controlled," similar to how a classified report would be treated, a congressional aide told CNN. The aide said it was evident from the recent briefing that the Coast Guard had no intention of telling anyone about the probe until it became clear CNN would report on it.

Then, in a remarkable move after CNN's report last month, the Coast Guard Commandant and the academy superintendent issued public apologies for mishandling nearly two decades-worth of sexual assaults complaints.

CNN examined the Coast Guard's investigation into the woman's allegations and extensive court documents from her case and found that her case not only shows how the Coast Guard routinely dismissed serious sexual misconduct in the past, but also how its failures continued to reverberate and undercut the agency's ability to hold those attackers and Coast Guard and academy leaders accountable years later.

Linda Fagan, the Coast Guard's first female commandant who took the helm after the operation came to a close, is slated to appear before a Senate budget hearing Thursday and will address the swirling controversy surrounding Operation Fouled Anchor, according to the agency. At the hearing, senators are set to press on how an inquiry that exposed so many cover-ups was, itself, covered up.

The woman whose allegations prompted the investigation said in an interview with CNN that she feels a combination of "hopeful and pissed" that issues, which should have been addressed decades ago, are finally being spotlighted at a congressional level.

"The system is so broken, it wasn't going to fix itself," the woman, who did not wish to be named because of privacy concerns, told CNN. "Why is it taking so long to hear us?"

The case at the center of the probe

Within weeks of expressing her frustrations to her colleague in 2014, the woman met with a Coast Guard investigator to recount the events of a Saturday night in February 1997. The incident may have occurred 17 years earlier, but what she says happened was still fresh in her mind.

Cadet Edzel Mangahas had been her friend, she said, when she awoke to find him in her bed, smelling strongly of beer. When he made unwelcome sexual advances, she said she rolled herself into a fetal position to protect herself. But Mangahas continued to grope her. Then, she said, he raped her as she begged him to stop.

At first, the woman said she decided against reporting what happened because she had seen fellow cadets report abuse "then later be processed for discharge as the men continued on in the service." She says she did tell a school counselor in the hopes of getting support, but instead the woman told her that if she continued to seek counseling she could be kicked out of the academy or lose her officer commission for mental health reasons.

So, she stayed silent.

A few months later, however, she learned that school officials were investigating Mangahas for allegedly raping another cadet, a freshman. She gathered the courage to report her own accusation against him. "I still remember how my tears felt as though they were burning scars into my face," she would go on to write of the incident in an official statement given to academy leaders.

The alleged assault of the freshman resulted in Coast Guard officials pushing Mangahas out of the service. Despite that action, Mangahas was able to receive his diploma and join the Air Force as an officer.

Outraged that Mangahas was able to remain in the military, the woman said she met with academy attorneys, Lt. Glenn Sulmasy, and Captain Thomas Mackell, questioning how he had been able to stay in the military. She said Sulmasy and Mackell then discouraged her from pursuing the issue any further — telling her she should instead focus on her graduation prospects, according to court records. Both men dispute her allegation.

Nearly 20 years later, the investigators working on the Fouled Anchor inquiry found the woman's signed statement among old boxes in the academy's law library. The boxes were labeled with Sulmasy's name.

As investigators dug deeper into the case, they gathered additional evidence to sustain the woman's allegations against Mangahas. In October 2015, he was charged with rape in Air Force court martial proceedings.

Mangahas was the first and only alleged assailant to face criminal or military charges as a result of the Fouled Anchor investigation. But a judge and then appeals court ruled that the government had waited too long to prosecute Mangahas and that the statute of limitations on his alleged rape had expired so the case against him was dismissed.

The ruling was a blow to the Fouled Anchor investigation because it meant prosecutors no longer had the ability to pursue criminal charges against even those alleged perpetrators accused of rape whose alleged conduct dated back many years, if not decades, earlier.

After Fouled Anchor came to a close, the Supreme Court ruled that there was no statute of limitations for rape cases brought by the military. But a Coast Guard spokesperson told CNN that the narrow Court Martial definition of rape from the 1980s that applied to the historical cases examined by the probe meant that the bulk of the alleged assaults remain off limits for prosecution.

Mangahas, who had been put on leave during the court martial proceedings, now serves in the Pennsylvania Air National Guard after his time in the Air Force, according to a National Guard spokesperson. The Air Force did not comment on the prior case against him.

Mangahas' attorney, Terri Zimmermann, was adamant to CNN that her client was innocent and said she believes that he would have been acquitted if his case went to trial. She said he had never been aware of the allegation against him until Fouled Anchor was underway. "How do you defend yourself after 17 years have gone by?" she said. She also noted that an officer at a preliminary hearing in the case had not found enough evidence to support moving forward with the case but the government had moved forward anyway.

"I'm sure there were women who were raped and they handled those cases badly ... It happens every day unfortunately," she said. "There are officers who went on to graduate from the Coast Guard Academy that probably should have been investigated and prosecuted earlier. I don't think Ed Mangahas is in that category."

'They set their precedent'

With criminal charges off the table, Fouled Anchor investigators turned their attention to finding any perpetrators who remained in the service to see if they could be held accountable administratively. But here, too, they found that the passage of time worked against them. Many of the suspects had retired or long ago left the Coast Guard.

There were a handful, however, who remained on the job. The Coast Guard ultimately pushed out two high-ranking officers who had both been in line for promotions when Fouled Anchor unfolded.

One of them had been investigated for sexually assaulting fellow cadet, Kerry Karwan, while at the academy in 1995. The alleged perpetrator, a football player, had come to her room to borrow her headphones but refused to leave until she stood up and gave him a hug, she wrote in a journal entry she later turned over during Fouled Anchor. She agreed, but quickly pulled away after feeling his erection. According to Karwan, he bit her neck and groped her breasts before leaving her room. He warned her it would be easy for him to return since she didn't have a roommate.

Unable to lock the door to her room due to academy policies, she "booby trapped" it before going to sleep that night, according to her journal. She reported the cadet to school officials the next day even though she knew doing so could expose her to backlash from others on campus. "I couldn't live with myself if I thought he was trying this (with) other girls," she wrote in her journal.

In the end, his punishment for his alleged assault included 75 demerits and an assignment to write a paper on the sexual harassment hearings involving now-Supreme Court Justice Clarence Thomas, according to records.

During the Fouled Anchor probe, records show that Karwan told investigators she had heard from other women who had been allegedly assaulted by her attacker while attending the academy. But they were too afraid to report what had happened after seeing how she was ostracized for coming forward, Karwan said.

"If they had actually looked into it the way they should have, other women would have come forward and said something," she told CNN. "Not only did they not handle it well, but then they set their precedent for how it was going to be handled."

Records show that the Fouled Anchor investigation into Karwan's alleged attacker ultimately looked into allegations from multiple victims, including one involving descriptions of rape.

While the Fouled Anchor investigation did not gather enough evidence to substantiate rape claims against him, investigators did find that he had committed indecent assault, but the statute of limitations prevented him from being charged in military court. The officer had been set to be promoted to captain, but instead, he was denied his command assignment and discreetly allowed to retire from the agency, according to records reviewed by CNN.

Confidential records reviewed by CNN show that within Coast Guard headquarters, officials had crafted a detailed communication plan aimed at keeping the action against the officer under wraps — directing Coast Guard employees that even requests for information from Congress should be declined.

"Evidence gathered through the Fouled Anchor investigation has led to a determination that the conduct of [the captain] while serving as a cadet at the Coast Guard Academy renders him unsuitable for command," a communication plan stated. "Without an overriding public interest in the result of an administrative action, such as the relief of a commanding officer, these actions are not disclosed publicly due to privacy concerns."

Years later, Karwan remains frustrated — that an alleged attacker was still able to retire honorably and that more wasn't done as a result of Fouled Anchor, which she says put her safety at risk by encouraging her to take part in a recorded conversation with her alleged attacker

"He is in the wrong, but I get to pay the price. I already endured retribution while at the Academy from reporting him the first time. I can only imagine to what levels of escalation this could be taken to," she wrote in a 2018 letter to the then-Trump White House about the investigation. "The Coast Guard has ignored me, used me, humiliated me, endangered me ... is this the 'justice' the investigation was supposed to achieve??"

Years of mishandling

As Fouled Anchor stretched on, investigators turned from looking at alleged rapists and other perpetrators to the academy leaders who had kept their reported assaults quiet.

Agents interviewed 20 people who had served as senior officials at the academy and had a hand in how the cases were investigated and resolved, though some key people had passed away, records show.

Ultimately Fouled Anchor found that the academy's leadership "did not adequately investigate allegations as serious criminal matters and hold perpetrators appropriately accountable."

Of 31 sexual assault allegations reported to the academy between 1990 and 2006, the Fouled Anchor probe determined only five had been reported for criminal investigations as required, according to a draft of the Fouled Anchor final report from 2019 reviewed by CNN.

They "failed to take sufficient action to ensure a safe environment - particularly for female cadets - and failed to instill a culture intolerant of sexual misconduct," the report stated about those at the helm in the 90s and early 2000s.

Despite such a damning conclusion, Fouled Anchor resulted in no punishments for those leaders.

"The ability to assign specific accountability was limited because none of these individuals remained subject to criminal or administrative actions, the evidence for the decisions made on these cases (most of which were over 20 years old) was incomplete, and the imprecise nature of the then-existing policies."

Mackell and Sulmasy, the academy lawyers who allegedly met with the woman whose allegation sparked Fouled Anchor for example, were not subject to any public action against them.

Sulmasy left the Coast Guard in 2015, and now serves as the president of Nichols College in Massachusetts. Sulmasy's attorney disputed that Sulmasy had pressured Mangahas' alleged victim, saying he "has no recollection of any such conversation from a quarter of a century ago, much less of having said anything that would discourage any cadet from putting another cadet on report for a serious criminal offense."

Mackell could not be reached for comment by CNN, but also disputed the woman's allegations in interviews with Fouled Anchor investigators, according to court records, saying that he would have done more with her case if he thought she wanted him to.

Congressional scrutiny

The Fouled Anchor investigation, which was supposed to shed light on past cover-ups and abuses, was in the end covered-up as well. The records remained confidential for years and it wasn't until CNN asked whether the agency's congressional overseers were aware of the report that the Coast Guard actually briefed Congress.

Karl Schultz, who led the agency when Operation Fouled Anchor came to a close, declined to comment to CNN, referring any questions to the agency.

Following the publication of CNN's investigation into Fouled Anchor, the agency's leader, Fagan, sent a rare apology to the tens of thousands of people who make up the Coast Guard's workforce.

"By not taking appropriate action at the time, we may have further traumatized the victims, delayed access to care and recovery, and prevented some cases from being referred to the military justice system for appropriate accountability," said Fagan, who herself graduated from the academy. "We own this failure."

But some members of Congress aren't satisfied.

"This episode is probably the most shameful, disgraceful incident of cover-up of sexual assault that I have seen in the United States military," Sen. Richard Blumenthal, a Democrat from Connecticut, where the academy is based, told CNN this week.

Democratic Sens. Maria Cantwell of Washington state, chair of the Senate Commerce Committee, and Tammy Baldwin of Wisconsin, meanwhile, sent a letter questioning both the lack of transparency around the probe and the lack of actions to hold both perpetrators and academy leaders accountable.

The senators are demanding a long list of information and documents related to the secret investigation, including the names of all substantiated perpetrators and academy officials investigated during the probe. A staffer with Baldwin's office said the Coast Guard has not yet responded to the letter's questions and document requests, though Baldwin plans to discuss Operation Fouled Anchor at Thursday's hearing.

The congressional aide interviewed by CNN said that staff has been researching potential actions, such as possibly stripping pensions from perpetrators, but that seeking accountability appears difficult because their pensions are written into law unless court martial convictions have been reached.

Several congressional offices are still looking at ways to prevent this from happening again, according to multiple staffers.

Sen. Chris Murphy, also a Connecticut Democrat, is working on ways to include transparency requirements in upcoming legislation and has been calling for "anyone involved in this cover-up" to be fired.

"For years, I have been calling on Coast Guard Academy leadership to be transparent about sexual assault on campus and get serious about reform," he said in a tweet, referencing CNN's investigation. "Instead, we now know they were deliberately hiding the truth."

Were you interviewed as part of Fouled Anchor or have something to share about someone involved? Do you have information or a story to share about the Coast Guard Academy or Coast Guard past or present? Email melanie.hicken@cnn.com.