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As far as anyone can tell, it starts somewhere in remote Russia; though whether by magic or mutant or something else, no one can say. It takes days to spread far enough into the country for the international community to notice, and it's such a strange situation that no one knows quite what to do.
Coulson hears about it only after the problem spreads to neighboring Ukraine, where three cities (and two SHIELD agents) disappear overnight. It takes two more days and eleven more cities—four in Romania, two in Poland, and five in Germany—for the phenomenon to become newsworthy in the United States.
SHIELD’s first thought is terrorism, but the cities themselves are left untouched—only the people are missing. In the time that it takes to send teams to each of the affected towns, eight towns in Spain have also vanished, along with half the population of Portugal. SHIELD’s next best guess is some kind of contagion, but if there is such a thing, it leaves no biological or chemical trace behind.
Those who believe that the vanishings are following some sort of pattern are proven wrong shortly thereafter, as the next four countries affected are Paraguay, Peru, Estonia, and India, which span three continents and share no borders.
It is at that point that Phil (internally; never, ever externally) panics. His immediate concern for Natasha—who is running an undercover operation in Latvia, a neighbor to Estonia—is eclipsed by the fact that Bruce is currently in India, and no one is able to reach him.
Phil is on a flight to India when two things happen, almost simultaneously: he gets a call from Natasha, explaining that she is on her way home, and he receives confirmation that the phenomenon has hit Texas. Within twelve hours, an equal number of U.S. cities have disappeared.
No one knows where the vanished have gone or how (or if) they can return, but it takes barely a week before too many people have disappeared for that question to truly matter anymore. As in every crisis situation, some people panic, but most of the world is frozen. The phenomenon has swept every continent (an international coalition of scientists disappeared from Antarctica less than a day ago), and though there are some countries that haven't been affected, others are experiencing their second round of vanishings. Citizens look toward their governments for action and reassurance, but there is none to be had. There is no enemy to fight, and no place to hide, because there is no rhyme or reason to who will disappear, when they will vanish, or which areas might next be affected.
Phil’s worry ratchets up again as the occupants of more U.S. cities disappear, and in states other than Texas. Unless circumstances have changed, only three Avengers are currently stateside: Tony is at the Tower; and Steve and Clint are in Oklahoma doing some pointless PR stunt that Phil curses even more now for having taken the pair out of New York. Natasha’s movements stalled somewhere in South America, and he still hasn’t located Bruce. None of the Indian towns that have vanished are places where Bruce usually works, but the “not that kind of” doctor generally goes where he thinks he's needed, so it's sometimes difficult to keep track of the man.
(Plus, Phil has no desire to tell Tony that he's lost his best friend.)
Phil knows it's irrational, but he actually worries for Tony the most, like the genius will be taken without Phil there to watch out for him (he’s going to disappear from the Tower and nobody’s going to notice because Tony is phenomenal at hiding, and so everyone will assume that he’s locked himself in the lab, but Phil’s going to go home and Tony will be gone—)
Just as Phil's about to work himself into another mini-panic, his phone rings. It's an unknown number, but Phil can't afford to not answer. He just hopes that whoever it is can't hear the utter exhaustion in his voice and will quickly get to the point.
“This is Coulson.”
A muted, rustling sound comes over the line, followed by a familiar voice. “Phil, it's Bruce. I could really use a pick up right now.”
Phil doesn’t bother to hide his heavy sigh of relief. The sooner he gets to the scientist, the sooner he can get to everyone (Tony).
“Tell me where you are,” he orders.
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It takes another day and a half to reach Bruce, who is tired and filthy but otherwise well, and then another ten hours for them to meet up with transport back to the States. Phil tries not to pay attention to the growing list of disappearing cities as time passes: Hong Kong, Nairobi, Milan, Sydney, Boston, Santiago, Prague. The litany of bad news is briefly cut off by a call from Natasha, saying that she’s finally crossed the border into Texas, but then the flood of worrying details continues.
The entire population of Maine has disappeared, along with significant portions of South Carolina, Colorado, and Wisconsin. By some miracle, Steve and Clint make it back to New York before Phil, so the man has most of his chicks (with Thor on Asgard, and Natasha still working her way home) safely in one place by the the time he makes it to the Tower.
Tony, Steve, and Clint are waiting for them when Phil and Bruce land, and the normally collected man is not the least bit ashamed for practically running into his husband’s arms and squeezing the genius like he might fade away at any moment.
It's okay though, because Tony—who has no doubt been having the exact same thoughts as his husband since this started—is squeezing Phil back just as tightly.
“J says that there’s nothing we can do,” the genius murmurs into Phil’s ear when the others have stepped away. “As much as it kills me to say it, we have to wait it out. Promise me we’ll wait it out together.”
Phil knows that even with all of them in the same place, a vanished New York is still possible. If JARVIS says that there’s nothing to be done, then he and Tony have exhausted every avenue (and likely invented some others in the meantime), and Phil trusts their analysis. They’re going to have to sit back and hope that this phenomenon—whatever it is—ends soon.
Maybe it makes him a bad agent, but with Tony in his arms, the thought that they might fail—that they’re powerless to stop whatever is causing the vanishings—doesn’t bother Phil as much as he thinks it should. As long as Natasha makes it home before anything happens, Phil will gladly vanish into nothingness with his family by his side.
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Natasha finally makes it home two days later, amidst news of losses in Munich, Addis Ababa, Oklahoma City, and Rio de Janeiro. She’s covered in muck, and there are lines on her face that weren’t there when she left for her mission. Phil knows that the two of them should debrief, but Tony herds Natasha away almost before the others have finished greeting her, and Phil can’t help but feel relieved that the genius has taken the option away from him.
(The two Avengers disappear for hours, only emerging from wherever they were hiding in time for dinner. The meal is an understandably quiet affair, and no one comments on the redness of Natasha’s eyes.)
Neither Phil nor Tony sleeps that night.
The next morning, Tony explains the situation to the rest of them; Steve and Clint both have to make emergency trips to the gym, and Bruce to his Hulk-proof room.
Natasha already knew.
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Over the next month, nearly a hundred new ghost towns emerge around the world, their residents never to be found. The Avengers watch with everyone else as the number of disappearances increases steadily at first, and then drops sharply to almost nothing. Only two towns vanish in the final week, but it takes another month for those who are left to start believing that the crisis has passed.
The world that remains is devastated, both economically and emotionally, but humanity is nothing if not resilient. People pick themselves up and start over.
The Avengers do the same. With the exception of Tony’s obvious (and necessary) philanthropic efforts, it’s difficult for all of them.
They’re unsure whether the age of superheroes can survive this new world; whether they are needed, or wanted.
(They are.)
It is only much, much later, after everything has calmed down and people are settling into their new lives (and with the help of a barrel full of Asgardian mead), that Clint will admit to Phil that he and Steve made it through Columbus, Ohio mere hours before that city vanished as well. Natasha will share the story of a place where children were harmed in the mistaken belief that it would spare the rest of the town. Bruce refuses to give any details about his time in India.
Tony holds him in bed that night while Phil’s body trembles with all of the words he can’t say aloud, not with fear and relief both still stuck in his throat, but Phil’s heart beats out a staccato loveyouloveyouloveyou that echoes in Tony’s own.