Decorated Navy SEAL Brett Jones had already survived two harrowing deployments overseas when, back in the states, his world came crashing down around him, all thanks to an answering machine.

It was the morning after a welcome back party, and Jones was calling to thank a fellow Navy serviceman who organized the bash. The man wasn't in, so Jones left him a message at his military office, and then he did something without thinking about it.

"I said, 'I love you' before I hung up," Jones told ABC News, recounting the story by email.

The man Jones had called was his longtime boyfriend and part of an entire life Jones had for years kept hidden from even his closest SEAL comrades and, even more importantly at the time, the Navy. This was 2002, nearly a decade before the end of Don't Ask Don't Tell, and a time when serving openly in any service as homosexual was forbidden. Jones said he had known he was gay since he was 6-years-old and had just decided to risk keeping the secret in order to serve with one of the most elite military forces in the world.

But those three words just about did him in. He said a woman in the same office as Jones' boyfriend at the time heard the message and reported it up the Navy's chain of command.

"That was all it took for the Navy to launch a full-scale investigation that lasted for months," Jones told ABC News.

Jones said the military pulled his hard-earned security clearance and "treated [him] like [he] was a criminal."

"It was one of the most difficult times of my life," Jones said. "It was so damn humiliating."

"Brett Jones served his country honorably," Navy spokesperson Greg Raelson told ABC News in response to a request for comment for this report.

A spokesperson for the Navy declined to offer comment for this report when contacted by ABC News Wednesday, but said he was looking into Jones' allegations.

Jones' SEAL team quickly found out, and though Jones said the special operations world is "ultra-masculine" and apt to paint the gay community in a negative light, actually most of his teammates were supportive.

"Of course there would be guys who would talk and whisper behind my back, but overall I received the best support one could hope for from their brothers," he said. "I will always be thankful for those brave SEALs."

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Jones eventually connected with SLDN, the association for actively serving LGBT military personnel, who called on the help of a Washington, D.C. lobbyist. A couple weeks later the Navy dropped their investigation. Jones had a reprieve but decided that when his end-of-service date next came up, he wouldn't try to stick around. As his Navy record shows, Jones was honorably discharged in June 2003.

More than a decade later, Jones, now with a husband and son, decided to break his silence to the world about his sexuality, because he is in the process of writing a book about his experiences that he believes could "possibly help someone struggling with who they are, or help people understand that diversity is one of the greatest gifts the world has to offer."

He is one of the first ex-SEALs in the relatively small special operations world to ever to come out so publicly, and he first spoke directly to that "ultra-masculine" community through SOFREP.com, a military website created by and for special operations veterans.

In the SOFREP article, and echoed in his interview with ABC News, Jones said just about the hardest part was lying to his fellow SEALs for so long. "I absolutely hated it when I did that," he wrote.

Brandon Webb, managing editor at SOFREP.com and a former SEAL from the same Basic Underwater Demolition/SEAL class as Jones, wrote on the website that he had no idea Jones was gay at the time, but it didn't matter.

"The people with whom I've worked in the Special Operations community are more concerned with an individual's contribution to the team, and their ability to do their job exceptionally well, than their race or sexual preferences," Webb wrote. "And while politicians and religious fanatics made a fuss about gays serving in the military, these men and women proudly served their country in silence, and earned the respect of their peers until DADT was eventually repealed… I am proud to call [Jones] my friend."

Jones' public revelation comes eight months after a transgender former SEAL, Kristin Beck, decided to come out publicly in her book "Warrior Princess."

READ: Transgender Navy SEAL 'Warrior Princess' Comes Out

Kristin Beck, who as "Chris" served 20 years as a SEAL, struggled with her sexuality while fighting alongside special operations warriors in some of the most dangerous places in world.

In her book, Beck says she "considered living as the woman he felt himself to be for a very long time, but while he was serving as a SEAL, he couldn't do it."

Jones told ABC News that he was "inspired" by Beck's courage to come out publicly. And so far, he has no regrets.

"Everything has had its purpose and has put me on the path that lead me to the most amazing husband and son anyone could hope for," he said. "God has truly blessed me."

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