Post-movie, so spoilers. And it turned sad somewhere. Sorry for that.
It all comes together, in the end.
Stark takes only a year to remodel his shining beacon of a tower to be tailored to an idea, an idea Pepper crazily enough supports of him. Maybe because right at the start of the remodeling project, Tony had made a plaque he planned to put somewhere. He wasn't sure then, at the time, and he still isn't sure now, but he keeps the plaque close so that when he does find the right place, it will go there immediately. (And Pepper loves the plaque; she almost cried, and they spent a night in some swanky penthouse hotel room curled up on a couch as she talked about all the moments Tony had missed or tuned out in the past.)
The world turned, as it did. The SHIELD agents still did their jobs around the world. Jane Foster is busy on her little science-y studies in some effort to reconnect Earth to Asgard, with the help of Stark grants and some employees who like cosmic shit, somewhere out in New Mexico, still. Steve Rogers is hunting down survivors of his era and doing volunteer work across the country, his way paid by SHIELD funds and Tony is not sure if he should change that or not. And Bruce Banner ran back to third world countries to do some semblance of life reaffirmation, but only after Tony wrangled a promise--a sworn oath, a verbal contract, a pinky swear--that he would come back when the tower was completed.
Tony still is not sure if any of them will return, but the modifications he can afford to make a hundred times over deserve to be done. Because of the plaque. And Tony is shaken to realize: he has faith.
Faith in an idea. It's scary.
The first to return is Steve, a duffel bag over his shoulder and his bike stored in a special garage cubby, because Tony is thoughtful like that. His apartment is pretty bare, full of the necessities with room for anything, though Fury mentioned gym equipment, so that is already there. Just in case and ready for use. Steve looks about, doesn't look like he really wants to personalize anything about the room--always a soldier--and must be verging on running, so Tony has to say something. "This is /yours/, Captain. It's home; make it one."
Steve stays.
The next are the assassins, with gear and suitcases and they both say there is no way in hell they are /living/ here, but a safehouse is not a bad back-up plan, if they need R&R from SHIELD. So they take up Stark's invitation and customize their apartments to the nines, weapons of all sorts that JARVIS catalogs for the sake of handiness, and Natasha does not like it, but Clint does. Clint also has direct access to the roof and Tony may or may not have made nooks and crannies for a hawk to nest in if need be all over the building, if it made him feel comfortable. Clint does not show it, but Natasha does, and she might have been thankful in her eyes when Tony mentioned it. But they are not here more days than they are, missions and all, but every time they come back, there is more stuff they are bringing.
Natasha and Clint stay.
It is almost a month later that Bruce finds his way back, tired and scruffy, with a thread-worn knapsack falling apart and honestly, he is met with surprise at his reappearance. Even Tony is a little shocked (and it might be a boost to his ego, too). "He made me pinky swear," Bruce explains, nodding towards Tony. "A man doesn't break a pinky swear." His apartment is just as bare as Steve's was, but Bruce is asking questions about it, the only one to really do so. Is it safe, what if I lose it, did you put in any sort of failsafes? "Not a one," Tony informs him, and Bruce looks ready to panic, but Tony rolls his eyes, because Bruce was insulted SHIELD had put in such a measure onboard the helicarrier (which is only smart, though very poorly planned, because how would they have gotten a transforming Banner to it at all?), and granted, that had been the bad vibe incident where everyone was sniping at each other, but still. So instead, Tony turns Bruce bodily to the right, points at a private elevator, and slips a cardkey in his hand. "But the lab does, if you care. And when you finally don't, the system can be disabled and removed."
Bruce stays.
Tony takes time to visit the apartment left for Thor from time to time. He was not sure then what an Asgardian would feel like and even now, with books of Norse mythology littered on a coffee table never put away, he still cannot fathom what it is like to be a god prince of ye ole traditions. But there is a very big balcony for him to land on, so he may not use the regular, human entrances if he so desired. If he would ever return.
But then there is the day that Thor does return, a great smile on his face as he lands on Tony's launch pad and half of them are not there to celebrate the arrival (Natasha is somewhere in Slovakia, Steve at a children's benefit in Central Park, Pepper is in Malibu), but they're all back in a few days, and it's been big inside dinners and too much drinking the entire time while Thor recounts events and glories and how Jane finally cracked the spacial code to make a Migardian bifrost bridge and why had Tony not heard of this? It was his funds and employees, after all.
But they are all home now, and Tony decides only now should he pull out the plaque he is still not sure where to put, because these people are crazy enough to consider themselves Avengers and it was all due to one reason.
Pepper scolds him, because she is about to cry again, and everyone looks a little remorse until Thor lifts his stein and bequeaths his traditions of why to honor the dead should not be sad, for it's true, we miss them, but great people are honored and honorable people are welcomed, and does not the Earth honor its fallen men with dignity and high spirits in their memory? "While you may not have halls for warriors in your beliefs," Thor says, "you do have a garden, I hear. A paradise. There is a time to be sad and a time for joy, and today shall not be sad."
Things get lighter again, after a clink of mugs and cans and glasses, because now Tony mentions his plaque dilemma and no one has any idea where it should go, either. Until Natasha looks up from her wine and asks, "You have more empty room, right?"
Tony looks to her, eyes narrowed in confusion at first, but then it is like every light in Rockefeller during Christmas lights up at once. He says nothing more.
The next day, Tony has metal, a sledgehammer, and a mess in front of one apartment, where he is fitting a new kind of door, one that opens and closes manually, so he can bore the plaque onto it without fear of it getting ruined because shit does not slide that way, Tony. A door with a knob and secret plans Tony has for the inside, and everyone gets a chance to admire its permanent place alongside them, and some are forming an idea of what Tony might be doing the day he is spotted dragging inside the room a dusty SHIELD case. "What better place," Tony remarks, "for these things than here?"
A glint of light flickers off a half finished shield prototype when Tony closes the door, and he eyes the plaque once more.
("In loving memory of Phil Coulson, who believed in heroes.")
It all came together, in the end.