Marvel's The Avengers: What If? is a 2012 one-shot What If? comic book taking place in a divergent reality from the Avenger's movie. The alternate reality is What If the Nuclear Warhead at the End of Avengers had destroyed Manhattan?
The comic begins as we see a news broadcast from Brooklyn, New York with the island of Manhattan in the background. The reporter tells says that there have been different reports of what is attacking Manhattan, the most far out of them being that it is aliens, but they do seem to be coming from a portal in the sky somehow. Some 'metahumans' also seem to be fighting the invaders. Among the heroes are the famous Tony Stark in his armor, the man calling himself "Thor" last seen in New Mexico, the hulking monster that previously attacked New York a few years ago, and Captain America himself who has not been seen since WWII. Suddenly, in the background of the news broadcast we see a nuclear missile hit Manhattan and destroy the entire island in a massive explosion.
One month later: The land mass previously known as Manhattan has been cleared of most, if not all, nuclear radiation and is safe for a team of SHIELD operatives to enter, but not with the proper gear and flashlights to see through the smoke. Among them is Nick Fury, the Director of SHIELD. After seeing the devastation, Fury simply calls Maria Hill (on the Helicarrier) on their cell phones, saying that he will resign from being Director of SHIELD after this (which is why he didn't use the communication system, because he's not part of SHIELD anymore). Nick Fury and the team of operatives find the bodies of Iron Man, Captain America, Hawkeye, and Black Widow, along with thousands of Chitauri and thousands of civilians who didn't evacuate in time. Suddenly, a giant flying Chitauri Leviathan rises up and starts attacking the SHIELD operatives. Thor, who survived the nuclear explosion, fights the Leviathan in the air, but it is Loki, who also survived, who kills the Leviathan, using the long broken off horns from his helmet as sword-like weapons which he now wields with deadly accuracy (and his skin is back to it's natural Frost Giant blue). Thor says that Loki is on the side of good now, and Loki warns that the rest of the Chitauri are going to try to invade again. So, Nick Fury, Thor, and Loki go on a mission to find the Tesseract, and the team of SHIELD operatives offer to help.
At the Pentagon, Lt. Col James Rhodes aka War Machine has his armor repainted red, white and blue by the government, because they say that America needs a heroic symbol now that the Avengers are gone, and is given the new codename Iron Patriot. Iron Patriot is sent to find the Tesseract before Nick Fury and the "rouge" SHIELD operatives can. It is believed that the Hulk, having survived the nuclear explosion, took the Tesseract to the nearest desert, New Mexico. Iron Patriot finds Hulk in a cave in New Mexico with the Tesseract. Hulk attacks him and tells him to go away, and Iron Patriot calls in Nick Fury's former council of superiors and tells them to get Nick Fury on the line immediately. Iron Patriot tells Fury to come to New Mexico and that he can't handle Hulk much longer. Fury does just that, but he (and Thor, Loki, and the team of SHIELD operatives) need a way to get there quick enough. Just then, the Helicarrier shows up, and a smiling Maria Hill (on the SHIELD communication system) tells Fury that every SHIELD operative has disobeyed SHIELD's council of superiors (who launched the nuclear warhead in the first place).
Soon, the Helicarrier arrives in New Mexico and Fury, Thor, and Loki parachute (with the exception of Thor) down to the ground and help Iron Patriot fight Hulk while Maria Hill (who also parachuted) retrieves the Tesseract from the cave while Hulk is busy fighting. But, Hulk easily kills Maria Hill, and Loki sacrifices himself to kill Hulk using the Tesseract. To Fury and Iron Patriot's surprise, Thor betrays them by bonding the Tesseract to Mjolnir and killing Iron Patriot by causing his armor to explode. Thor then shoots a blast of energy at the Helicarrier, causing it to crash on Nick Fury and explode, leaving Thor the only one alive.
Thor then destroys the Tesseract, Mjolnir, and himself by causing the Tesseract to explode itself in a blinding burst of energy.