Transgender teen, second-grade counselor reunite years after life-changing friendship

A decade ago, a second-grade student made a bold statement. The student passed out notes to classmates reading, in scribbled crayon, "I am a boy" and "I am not a gril. [sic]"

Now a high school graduate, Nathan Jones is thanking the counselor who encouraged him to be himself so many years ago.

"I've always felt like I've had a boy's brain," Nathan said. "And I always felt like I was trapped in this girl's body."

Nightline's Juju Chang has been following Nathan for four years. The Jones family allowed cameras to follow Nathan's transition -- a metamorphosis, Chang called it, from an awkward and seemingly depressed 14-year-old into a confident and charming nearly 18-year-old man.

WATCH THE FULL NIGHTLINE STORY ON ABCNEWS.COM

Nightline was there when Nathan changed his name from Natalie (a pseudonym) and when he underwent "top surgery" (a double mastectomy). They were also there for the moments every teenager experiences, like when Nathan began driving and when he graduated high school.

Nathan's road was not easy, Chang wrote. The suicide rate among transgender youth is 41 percent, and Chang wrote that it can often be linked to a lack of support by parents or peers.

"Nathan, too, was teased and physically bullied in school until he eventually decided to be home schooled," Chang wrote, explaining that he had a supportive home environment.

Had it not been for having parents who allowed his transition, Nathan said, he might have become a part of the suicide statistic.

"I know that if I had to live as a girl now, I most likely be very depressed," he said. "Hopefully not, but I most likely would have tried to kill myself."

As Chang's time following Jones came to a close, though, he surprised her by naming someone besides his parents who encouraged him to be himself from a young age: that counselor from the second grade.

So Chang decided it was time for a reunion.

Nathan explained of Amy: "She said to me: 'There's other people like you and you're not alone.' So I always thought that was the most profound piece of advice ever. It kept me going from second grade on."

Nathan was first sent to Amy's office on the day when the young student passed out the notes to the class. Their relationship blossomed from there.

Amy remembered Nathan well. So well, in fact, that his file is the only student's file that Amy kept from her 20-year career.

"I couldn't do anything big, but I could be there every day when Natalie needed to talk," Amy explained.

And those conversations made all the difference, Nathan said.

"You never made me feel like I was wrong and so many people had made me feel like I was wrong," he said of Amy. "But I got so much comfort in having you."