Ten stories above Manhattan, Zachary Quinto leans back in a chair, inches away from a massive plate-glass window. His black hair is gelled and a black T-shirt hugs his chest beneath a fitted black suit. We’re in a hotel suite for a press junket, but the view of the city skyline is so spectacular and Quinto’s look so unintentionally villainous that it feels like this could be a set-up straight from his new movie, Hitman: Agent 47, based on the popular video game series.

Hitman, with its intrigue of genetically engineered killers (Quinto and the English actor Rupert Friend) vying to either save or destroy the life of a mysterious young woman, taps into something of a Quinto speciality: ambiguity. He’s in town on a brief hiatus from the months-long shoot for Star Trek Beyond, the third film of the rebooted franchise, and will soon head back to Vancouver to trade in his five o’clock shadow for the smooth skin, pointed ears and bowl cut of Spock.

Beyond physical transformation, though, it’s Quinto’s ability to be an emotional shape-shifter, the charmer who might also be dangerous – or the implacably stoic half-Vulcan who’s somehow an amazing friend – that’s really distinguished him since his breakthrough role as serial killer Sylar on the sci-fi series Heroes.

The 38-year-old uses the same deftness he brings to his work while navigating public interest in his private life. In 2011, after much speculation on his sexual orientation, he told a New York Magazine reporter that, “as a gay man”, who was then starring on Broadway in Tony Kushner’s Aids-epidemic play Angels in America, he’d been struggling to reconcile the fact of New York legalising same-sex marriage in the same year that a gay teen, Jamey Rodemeyer, had committed suicide due to bullying.

Zachary Quinto in Hitman: Agent 47 Credit: Reiner Bajo

It’s clear that Quinto had planned what he wanted to say (“it was motivated by those kids who were taking their lives”, he tells me), but hadn’t alerted the magazine in advance. “Yeah, he had no idea, poor guy,” says Quinto, of the reporter. “He was like, 'Uh, what?’ I could see him register what I had just said and he was like, 'Oh my God, I might have just gotten a scoop,’ which he did. I didn’t tell anybody that I was going to do that. I wanted to make sure it was on my own terms and my own time.”

The payoff is getting to be freely affectionate with his boyfriend, model and figurative oil painter Miles McMillan, 25, even as they’re stalked by paparazzi. They met at a party two years ago and recently bought a loft together. The night of our interview, the couple went to see Quinto’s ex, Jonathan Groff, perform in the smash Broadway musical, Hamilton, then put on costumes and rimmed their eyes with black liner for Madonna’s gipsy-themed 57th birthday party in the Hamptons.

Hollywood has come a long way since Rupert Everett declared that coming out had torpedoed his career. “For me, personally, it’s interesting,” he says, “because I looked around when I got Star Trek, and I said to myself, 'Who could I look to for guidance for how to navigate this path that I’m on?’ And there wasn’t anybody.” Now, six years after the first Star Trek film, Quinto’s casting in a big-budget summer blockbuster again puts him in a league of one. “I look around and say 'OK, yes, there’s a lot of gay actors that are open, many more now than there were 10 years ago,’ ” he says. “But I still feel like I’m occupying kind of a unique space.”

Quinto has already overcome typecasting once in his career; coming off four seasons of Heroes, he knew he’d have to create opportunities to show off his range if he wanted to play more than a sci-fi villain. That’s partially why he co-founded the production company Before The Door Pictures, whose first feature was the 2011 financial crisis thriller Margin Call. Quinto plays a young risk analyst in the film, which ended up being nominated for an Academy Award.

Zachary Quinto (centre) produced and starred in 'Margin Call', which also featured Stanley Tucci and Penn Badgley Credit: Jojo Whilden

If that film showed his cerebral side, then Hitman demonstrates that Quinto knows how to kick ass. Both he and Friend did most of their own stunts, including tumbles off tall scaffolding. The onscreen bitter rivals became good friends in the process. “Yeah,” says Quinto, “nothing like beating the s--- out of each other to bring you together.”

He’s developed a similar kind of camaraderie with his Star Trek cast mates, which has been helpful as the franchise moves from director J J Abrams to Justin Lin (who’s done three Fast & Furious movies). He doesn’t share many scenes with his good friend Chris Pine, who plays Captain Kirk, instead spending most of his screen time with Karl Urban’s Bones. “Those characters are so diametrically opposed that it’ll be nice to see them interacting,” he says.

Quinto’s greatest takeaway from Star Trek is his friendship with the original Spock, the late Leonard Nimoy. Grabbing lunch together every week or two to talk about the character, says Quinto, eventually “became secondary to the fact that I just enjoyed spending time with him and I recognised a lot of qualities in him that I aspired to and I found him incredibly generous and intelligent and compassionate and funny”. He also grew close to Nimoy’s wife and children. “Leonard and I were like family, absolutely.”

Quinto was in Munich for the first day of rehearsals on Oliver Stone’s forthcoming Edward Snowden biopic, Snowden, when he got the news that Nimoy had passed away from lung disease. “I knew that Leonard was leaving the world imminently,” says Quinto, but, “Leonard wanted me to focus on my work and take care of myself.”

Zachary Quinto as Spock with Chris Pine's Captain Kirk in Star Trek Into Darkness Credit: Zade Rosenthal

Snowden is a chance for Quinto to showcase his dramatic chops while indulging his political side. He plays journalist Glenn Greenwald to Joseph Gordon-Levitt’s Snowden. Stone didn’t encourage the actors to consult with their real-life counterparts, but Quinto studied Greenwald’s writing and TV appearances. He also watched Laura Poitras’s Oscar-winning documentary Citizenfour a number of times. Stone’s picture, Quinto says, uses the structure of the hotel meetings between Snowden, Greenwald, Poitras (Melissa Leo), and The Guardian’s Ewan MacAskill (Tom Wilkinson) as a portal for flashbacks that tell the story of Snowden’s life leading up to his decision to expose the NSA’s illegal wiretapping.

“I thought it was really remarkable that it all started because he was a patriot,” Quinto says. “Say what you will – I know it’s a contentious issue – but for a 29-year-old guy to wilfully and knowingly give up his freedom and give up the life that he has become accustomed to for the betterment, as he sees it, of his fellow citizens I think is really admirable.” As for Greenwald, Quinto finds him, “fearless and relentless to a degree that is very exciting to me”.

A vocal Barack Obama supporter in the last two elections, he’s undecided on whom to support in 2016. “The notion that we’ll have potentially another presidential election with a Bush and Clinton against one another is disgusting to me, actually,” he says, “and I think is indicative of the dysfunction and corruption of our political system, and the fact that there’s virtually no difference between Democrats and Republicans.” Clinton, he says, is merely “the devil you know in that scenario”.

For now, though, he’s got a more immediate future to contemplate. He’ll be done with Trek in October and hopes to take a breather to figure out, creatively, where he wants to go next. “I’m kind of done with the villain moment,” he says. Not that he hasn’t enjoyed his iconic roles, but he’d like to explore other things, like comedy and theatre; he was last on Broadway in February 2014 for The Glass Menagerie and his goal is to get back onstage within a year.

Quinto seems secure in the knowledge that, unlike some of his openly gay predecessors and peers, he is eminently employable. “I work more now than I ever did when I was in the closet,” he says, “and I’m doing a wider range and variety of roles than I ever did before I came out. I feel like that’s what I need to keep demanding of myself and what I need to keep demanding of the industry.” After all, who would dare to to mess with a guy who can handle a gun and do a Vulcan mind meld?