Some time ago, the Illuminati had discovered that entire universes were being destroyed in events called incursions in which the two universes, centering on Earth, would collide and destroy one another. They had done everything they could think of to stop the incursions, sacrificing their very souls in the process, but the more they tried, the closer they came to the realization that there was nothing they could to stop the wholesale destruction of the multiverse.
Time Runs Out takes place 8 months before Secret Wars and 8 months after AXIS, the countdown for the end of everything having already begun. The Avengers have come under the command of SHIELD, the organization now lead by Sue Storm and Steve Rogers, both trying to find the Illuminati and bring them to justice. To make matters worse, the new Cabal, led by Namor, is still out there, destroying worlds to save their own, a tactic Namor himself had used before the Illuminati cast him out. Sometime during the 8 months of AXIS, Tony Stark was captured by the Cabal, and forced to help them with their plans. The Cabal has also taken over Wakanda, and has been using it as a base from which to seek out other universes and destroy them to save their own. Meanwhile, Dr Doom has allied himself with the Mad Thinker to map the multiverses and discover the source of this collapse. Meanwhile Sunspot is leading his own group of Avengers, who had bought AIM and using their resources to find a possible solution. But no matter what the heroes and villains, in many ways indistinguishable from each other now, do, the White Event was still approaching, and universes are still dying.
Using AIM resources, Sunspot manages to build a device to track the source of the decay of the Multiverse, and the Avengers send a team lead by Odinson and Hyperion to find it. They encounter the Black Priests, who are also trying to save the multiverse under the leadership of Doctor Strange. Together they form a plan to capture a Black Swan from Rabum Alal in order to capture one of the Ivory Kings’ Mapmakers. The Avengers and Black Priests subsequently split up, the former going for the Black Swan, the latter going for the Mapmaker.
Back on Earth, the Illuminati allowed themselves to be found by Rogers and SHIELD, only to lead them into a trap. Sunspot arrived, siding the Illuminati and pleading with Rogers that they need to put aside their differences and work together to end the incursions. Rogers refuses, and deploys the Mighty Avengers, sparking a massive battle between. Eventually, Sue Storm reveals herself to be working with the Illuminati all along, and traps everyone in force cages. There, the Illumanti, now joined back Black Bolt, a repentant Namor, and Medusa, tell the Avengers that they have to deal with the Cabal before they destroy any more worlds.
Leading them to another universe, Namor sets the trap for the Cabal, leaving them on a dying universe. However, Black Bolt and Black Panther prevent him from leaving, ensuring that he pays for his crimes before they return back to their reality. What they didn’t know was that the Cabal detected another oncoming incursion, and jump to that reality, the Ultimate Universe, and encounter the Maker, and make him aware of the incursions.
On Earth 616, every group of Avengers and the Illuminati meet to discuss a solution, getting nowhere. One thing that was clear was that the incursions were accelerating, with only a few dozen realities remaining. Yellowjacket contacts them then, stating that he has found the source of the incursions, and that the Ivory Kings were in fact the Beyonders! The Beyonders were killing each universe’s Celestials, which were causing a chain reaction and splintering the universes. Inspired by Reed’s daughter Val, the Illuminati began working on a life boat to escape the destruction of their universe.
Out in deep space, Sunspot’s Avengers and the Black Priests continue their search. The Black Priests track down a group of Black Swans, but are destroyed to a man with the exception of Doctor Strange, who is brought before Rabum Alal, who then reveals to be Doctor Doom. Doom explains that he and Molecule Man had travelled back in time, discovering the Beyonders’ plans to destroy the universes. Though he had managed to delay them, when he directly confronted the Beyonders, he was defeated, leading to the destruction of hundreds of thousands of universes, leading to where things stood now. Elsewhere, Sunspot’s Avengers do manage to find the Ivory Kings, and manage to destroy them despite heavy losses. Odinson and Hyperion were all that survived, but they met their end when countless Beyonders arrived to finish them off.
To make things worse, the Shi’ar had discovered that Earth was the centre of the destruction of the Multiverse, and moved to destroy it. The Illuminati and their allies moved to stop them, but were stopped at every turn until the Illuminati managed to phase a rogue planet around Earth to protect it. Iron Man, having escaped from the Cabal, then charged and fired Sol’s Hammer, destroying the Shi’ar fleet. On the Ultimate Universe, the Cabal and the Maker, contacted Nick Fury to inform him about the Incursions, who then readies SHIELD for a war with the 616 reality.
In the final moments before the last incursion, the Illuminati loaded as many people onto their lifeboat while Steve Rogers and Iron Man fought it out one last time. The SHIELD Helicarriers from Ultimate descended down on 616, the Avengers fighting them off until the last moment when the incursion hit, destroying both universe, Tony and Steve dying fighting each other as it all went down...
Time Runs Out was the last steps towards a calamity that Marvel, specifically Jonathan Hickman’s Avengers books, had been building to since the end of Avengers vs X-Men, some say even longer than that. The detailing of the end of the multiverse was so exquisite that it was one of the most tragic, and most harrowing tales in Marvel history. But it was all a precursor to a larger event, one that would rip the Marvel Mutliverse apart, literally, and change the company irrevocably like it had never been before.