A woman in the same office as Jones' long-time boyfriend overheard the telephone call and informed the Navy's chain of command. As a result Jones had his world came crashing down on him. He kept his sexual orientation hidden from everybody and this was his closest guarded secret. Brett Jones discovered he was gay since he was 6 . He decided to keep this a secret as he wanted to serve the Navy and back in 2002 serving openly as a homosexual was forbidden.
The man had his security clearance removed and soon felt as being treated like a "criminal". Jones said: "It was one of the most difficult times of my life. It was so damn humiliating". On the other hand his team-mates were supportive. Jones related about this: "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. I will always be thankful for those brave SEALs."
The Navy dropped the investigation against him and according to their records Jones decided to leave during his next end-of-service date. He was honorably discharged in June 2003.
Now, after nearly a decade later, Jones breaks the silence about what happened and is in the process of writing a book of what happened and how he handled the situation he was in. He hopes that the book 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."