Nate and his family agreed to do this story in the hopes that it will help people understand transgender issues, but they are also concerned that it will leave Nate exposed and vulnerable. WBUR has agreed not to publish the family's last name.

"This is a big challenge to a lot of people," Tom says. "And that’s where it gets scary. When people don’t understand things, that’s when they get the most uncomfortable and we don’t know what they’re capable of. So I want to follow Nate around everywhere and just say, 'Wait a minute, don’t even try that.' But of course that’s not possible."

Nate’s parents, who are divorced, and his stepfather are trying to understand and accept Nate’s decision, but they are worried and scared.

Nate had never heard the word "transgender" before he got to high school. But once he did, and figured out what it meant, "I was just like, 'Oh my God, that’s exactly how I’m feeling.' When you’re trans you just know. It's not something like..." Nate pauses. "I don’t want to be like this. Who would choose this?"

"I felt so wrong as a female, it was just so wrong, and there was so much I didn’t like about myself," he says in a soft, steady voice.

As far back as he can remember, Nate, of Boston, was uncomfortable as a girl.

"That’s where I started it," he says. "And then it just kind of took off from there. It was just like, no, I’m a boy."

The hood is part of a costume Nate plans to wear to the next meeting of his cosplay , or costume role-play, group. There are cosplay chapters all over the world. Nate’s is based on a Web comic called "Homestuck." His transformation from Natalie to Nate began two years ago, when he put on a blue men’s suit and boots, and gelled his hair into thick loops.

"I’m going to do the hood and worry about the cowl later," he says without looking up.

"Yes," says the 16-year-old, with an "s" that lingers. "OK, I’m gonna keep going, it’s not stuck."

BOSTON — Nate leans in, his broad shoulders hunched, his brown bangs almost touching the sewing machine bulb.

"I was just like, 'Oh my God, that’s exactly how I’m feeling.' When you’re trans, you just know."

Last year, Nate cut his straight brown hair short, started wearing a thick elastic binder to compress his breasts, and gave away his “girl” clothes. Even as Natalie, he’d been wearing a lot of flannel shirts and jeans. Nate has not had surgery to flatten his chest, nor has he started hormones that would produce new facial and body hair, more muscle and a deeper voice.

He still loves the high notes his female vocal cords can hit, but when speaking, Nate very consciously drops his voice into its lowest range to try to sound male.

"My vocal tone, the way it’s deep right now, this isn’t natural," he says. "My natural voice is — no, we don’t talk about that."

Nate’s parents say they weren’t shocked when Natalie yelled, during an argument, "I’m a boy," but they didn’t exactly see it coming either.

"I think she kind of dropped little hints," says Jackie, Nate's mom. "It’s amazing to me that I didn’t even realize that."

Maybe Jackie didn’t realize what was happening in part because she and Tom tried not to raise stereotypical girls. Nate has a younger sister.

"I thought, if I have girls, dammit, they're going to be coolest, toughest, no Barbies, none of that crap, you know?" Jackie says laughing.

And it's not like Nate loved sports, Tom says, or other traditional boy things.

Natalie, who now goes as Nate, dancing in a backyard in Medford in 2007. (Courtesy of Nate's family)

"[He] actually loved to wear really like outrageously flashy feminine dresses," Tom recalls. "Back when Nate was born, I wanted to dress her in gender-neutral clothes, so, man, what did I do to help influence this process?

"Would it have been different if we’d said, 'You’re only going to wear pink like other little girls and you’re going to play with Barbies.' I gotta think, was that the right thing? Maybe it was, maybe it made it more comfortable for Nate to become Nate, I don’t know," Tom says, shrugging.

One of the most difficult issues for Tom is whether he should behave differently with Nate as his son.

"I’ll go to give him a big hug or something and he kind of shrinks back," Tom says with a sigh. "And I’m like, oh, is that not something I’m supposed to do anymore because [that's] something I’d do to a girl and not a boy? I don’t call you sweetie anymore. I guess those things happen as your kids get older, but how differently would I have treated him if he was born a boy, physically?"

Nate's parents have an endless stream of questions: Is Nate rejecting life as girl after being bullied by a clique in middle school? Is Nate really a tough lesbian, as he seemed to be at age 14? Or, Jackie asks, "Is this something — I feel terrible saying it — is it a phase? Are you going to change your mind in a few years?"

Sitting next to his mom on the living room couch, Nate bristles.

"Not that many years ago," Nate says, admonishing his mother, "people would come out as gay and they'd hear, 'Oh, it’s just a phase.' It’s exactly the same thing as that, so it’s just kind of, even if you don’t mean it to be offensive, it can really be a little bit rude to call it a phase."

"Absolutely," Jackie says, interrupting Nate and nodding vigorously. "I remember my mother asking the same question about a cousin 20 or 30 years ago, so when I hear those words coming out of my mouth about this I do feel a little bit like I’m just not catching up, I’m getting old. But you’ll probably be a parent one day and you’ll see, you can’t help saying... Is there something I’m missing here?"

These are heavy conversations, but the family can already look back on some changes and laugh.

"I noticed that my underwear drawer does not get raided any longer. Nate has his own underwear," says Nate’s stepfather, Wes, who’s been listening quietly from across the room.

Nate screams with embarrassment and laughter.

"My jackets still disappear," Wes adds.

"Cause you wear nice clothes," Nate says in a voice that pleads for understanding.

Difficulties With Pronouns

Nate’s family is getting some help navigating all these changes. Nate sees a counselor at a center for gay and transgender teenagers through Fenway Health.

"But there’s not a whole lot out there," Jackie says, to explain "what this is, you know, why, why all the numbers now, why, why?"

A 2011 report out of the Williams Institute at UCLA Law says three in every 1,000 people are transgender. That would translate to about 20,000 Massachusetts residents.

There's no firm proof that transgenderism is a growing phenomenon in Massachusetts, but many parents, school administrators, counselors and employers will tell you it is.

At one of Nate’s cosplay meet-ups, about 100 people painted gray or blue, with colorful horns or wings, dance around a statue on Boston Common. When I say I'm writing a story about young people who are transgender, at least a dozen yell, "That's me!"

"I’m transgender," shouts one person who looks like a boy in a blue spandex costume. "So am I," says a teenager who might be female. The person behind her yells, "We all end up here."

But transgender is just one way these young adults are redefining what it means to be male or female. Rue Hartsell, a student at the Art Institute of Boston, identifies as genderqueer. Rue goes back and forth between male and female, depending on the day or the moment.

"A lot of my friends use 'she,' a lot of my friends use 'he' for me," Hartsell says. "Honestly, I kind of like people not knowing. I like people not being able to tell. That actually feels a lot more comfortable to me."

Nate is practically giddy with excitement in this crowd, where he doesn’t have to explain himself.

Nate and his friend Devon on Boston Common during a cosplay meetup. (Martha Bebinger/WBUR)

"I know almost half the people here really well. This is family," he says with a wide smile.

At home, with his biological family, life is not so easy.

"It's hard now because Nate always feels rejected," Jackie says. "I mess up the pronouns and am not making the transition as quickly as he would like."

Jackie says she’s trying, but remembering to say "Nate," “he” or “my son” is difficult.

"I mean, you say Natalie 100 times a day for 16 years," she says with a sigh. "You say, 'Wake, up Natalie,' you say, 'Natalie, Natalie, Natalie, Natalie.'" The name rolls off Jackie's tongue like a song. "Now I’m trying to go to Nate. But I get talking, the 'he's' are just..." Jackie doesn't finish the sentence. "I think it’s because I don’t see him as a boy, I just see Natalie, just Natalie, my kid, Natalie."

Jackie and Tom both notice the spark in their child's eye when people call Nate “he.”

"I try to do that and I know that half the time I totally blow it," Tom says, hitting his hands on the arm of his chair. "And then I start thinking, 'Oh, you know, there goes that moment I was trying to be supportive. I was trying to do the right things and I just blew it again.'"

'Gender’s Weird'

One more element of Nate’s life as boy: He's attracted to women and calls himself heterosexual. Nate has someone he calls his “partner,” a biological female who goes by the pronoun “they.”

If you're confused at this point, maybe you'll understand why Jackie asks Nate if he could describe, in advance, the friends he’s bringing home.

"Especially," she says to Nate, "when you’ve got six or seven kids in the room and I’m not sure of any of their, their... Sometimes I just need some hints. Is that a boy or is that a girl?"

Jackie looks at Nate. "And I don’t think you even think that way."

No, Nate says, "I don’t." He looks down and whispers, "Gender’s weird."

His parents look at him, stunned, and then explode.

"Did you hear that?" Jackie shouts. "She [Nate] just said gender’s weird. That’s the point, gender’s weird."

But what does Nate mean by that?

Gender isn’t just male or female, he says. "Gender is so complicated. Once you actually get in depth with it, you’re like, whoa, there’s a lot of things that I had no idea existed. It’s kind of confusing — even for me sometimes."

WBUR reporter Martha Bebinger will moderate a live chat at noon on Friday, Jan. 24 to answer any questions you might have about transgender or genderqueer issues. Ask your questions in advance here.