It isn't like in those stories, the ones where the protagonists have their first kiss and suddenly they're having sex. No, it's much more intricate than that. It begins with their friendship.
From the first time they meet, Bruce knows he and Tony are going to be good friends. He can't see their potential, assumes the team will kick him out before anything consequential will happen, but he shakes Tony's hand and knows they've got something as Tony compliments him on his work...and then his tendency to turn into a green rage monster.
Their first kiss is casual, something between friends. It happens over work; they've finally cracked a code and are laughing happily, Tony's arm around Bruce's shoulders where he'd placed it as he stepped up behind Bruce. The latter turns his head, forgets how close they are, and their laughter dies off, but their smiles stay, just a bit softer. Then they lean in, press their lips together, and that's it.
Kisses between them become very regular. There's 'hello' and 'goodbye,' and then there's 'good work' and 'wow, that was fun.' It's a ritual that only the two of them share, and maybe it's a bit gay, but both of them are straight and besides, they're best friends. The team didn't question it, though the first time they'd seen had been quite a shock; Clint had fallen from his perch, Thor dropped his hammer on his foot, Steve had turned bright red, and Natasha just raised an eyebrow.
At some point during the first year, they begin sharing a bed. Holding one another while they sleep just comes naturally to the two of them, so it only makes sense that they protect each other from their nightmares.
After two years of this, something changes. Tony shuts Bruce out for nine days, nine torturous days for the two of them, but Tony knows the end result will be worth it. When he finally allows Bruce to override the doors, Tony holds out a wrapped black box with a purple bow. He looks exhausted, but the smile on Bruce's face when he explains is definitely worth every second. It's his birthday, though the man himself forgot, and Tony's present? Pants that stretch when he Hulks out. Bruce laughs, says he loves it, and then leans in and kisses Tony. There's a small spark of something, and Tony gasps, Bruce drops the box, and then, wow, they're exchanging laughter and air between gentle kisses. 'Did you feel that?' 'Yeah, you?' 'Yeah.'
According to the team, they've always been together, but this doesn't stop the smiles they get when they walk into breakfast hand-in-hand.
They don't have sex for a long time. Which, y'know, is saying something for Tony, but they work together so well that he doesn't even have a thought of going to someone else. Their first time is terrifying for Bruce, who is scared he'll Hulk out, but maybe Hulk knows how much Bruce loves Tony, because he doesn't make an appearance, except for Bruce's eyes flashing green as he climaxes. They lie together afterwards, curled around each other, and fall asleep.
It's six years into their friendship, three years into their relationship, and Bruce proposes. Tony says yes, of course he does, and they get married right in their backyard, surrounded by their friends. Only one story comes out of it, but it seems so far-fetched that no one believes it. They always wear their rings, simple gold bands engraved with the other's name on the inside, and never addressed the press about their relationship, so they continue this tradition into their marriage.
Twenty years after they meet, Tony gets into a car accident. He'd been on his way to pick up Bruce when he saw the other car on the road swerve drastically. Tony'd yanked the wheel and wrecked his Mustang keeping the other car from reaching Bruce, who dropped his bag and ran at the mess of metal. Bruce is too terrified to get angry, but he hits the emergency button on his phone and JARVIS is calling an ambulance. He pries the door open, thanks Big Guy, and holds Tony's hand and tells him everything's going to be okay, he can't die now, not when they're both only starting to go gray and they have so much more to do, and Tony just smiles through the pain, says he'll be alright.
In the end, he is alright, though quite a bit beaten up. He's on bedrest for a few weeks and his arm is broken from using it to shield himself, but Bruce is just glad he's alive.
They're old and gray now, and look back on their days as the original Avengers with fondness and, yeah, occasional sadness, but those were good times, they agree. They found each other because of the Avengers Initiative, and that alone makes it a happy memory. Bruce rarely Hulks out anymore, though he does let the Other Guy out once in a while because he gets restless and pokes at Bruce's mind until Bruce gives in.
Tony is the first to go. To be honest, it isn't all that surprising. He'd gotten cancer a couple of years previous and Bruce gave in one night; Tony had asked him before but the doctors were working so hard, and Bruce gives him the pill anyway. He held Tony's hand and kissed him and held him close. They pretend Tony's just taking a nap, like he usually does because he gets so tired. Bruce cries. The Other Guy mourns- Hulk like tiny tin man.
Clint had questioned Bruce at his own wedding years ago with Coulson, watching Bruce smile at Tony from across the room during the first year of their relationship. "So, men do it for you?"
"Not men," he replied with a smile at Tony tapping on his reactor. Bruce turned back to Clint. "Just him."