It would seem the return of the formerly believed-to-be-dead Hercules would herald joy for the world, but instead he brings grave warning to the heroes of the world. Brought back by the Prince of Power; Amadeus Cho, Hercules, with Thor and Cho by his side, lead an army of heroes to face the looming multiversal threat of the Chaos King who had and was attacking, killing and consuming the power of all the gods and god-like beings from all pantheons and dimensions across the multiverse in an effort to consume and absorb the entirety of the multiverse to return it to it's original state; pure chaos. When Hercules lead the heroes for their initial attack on him, the Chaos King incapacitated the heroes and all the citizens of the world by using Nightmare's dreampower, leaving no one but gods and other god-like beings to oppose him. Hercules and Thor, with the help of Amadeus Cho, brought together a new incarnation of Herc's former team, the God Squad to defend reality and devise a way to stop the Chaos King.
The Chaos King solidified his hold on the universe with more gods of the different pantheons as they fall to his power. Soon after gaining control of all the various realms/aspects fo the underworld, he released the lost souls of countless dead people including the dead members of Alpha Flight, Avengers, and the X-men. With the influence of death removed from the universe, dead heroes and villains alike return to the land of the living, with many choosing to fight either for or against the Chaos King. In the end, it all comes back to the Chaos King as he now fights the only one left to stand in his way; the new, All-Father Hercules. The two adversaries battle savagely on a scale that dwarfs planets. With space and time crumbling as there fight rages, Amadeus instructs Hercules to punch the Chaos King into a pocket universe (the Continuum) where he is now alone as the be-all, end-all which made him believe he had won. The multiverse, however, had been laid waste by the Chaos King's war upon it and was now in shambles. Realizing this, Hercules, in what would be his last act as the all-powerful God of Gods, used his omnipotence to repair and restore the multiverse to it's proper state. Unfortunately, the act of doing this was so incredibley difficult it required every bit of godly power and might he possessed, leaving him fully and completely mortal afterward.
After coming back from his apparent death and becoming All-Father, Hercules senses a terrible evil, the Chaos King, approaching the Earth. Raising back to his old power of Anti-Eternity, Amatsu Mikaboshi has killed many alien pantheons, including Old Gods of Zenn-La and Shi'Ar, as well as Impossible Man and Nightmare, Lord of Dreams. When Hercules tries to unite Earth's heroes against him, Chaos King uses Nightmare's powers to put every mortal on Earth into a coma.
While few remaining heroes, Hercules, Thor and Amadeus Cho, are dealing with chaos and gathering new forces against him, Chaos King invades afterlife, killing, absorbing and enslaving multiple lords of Hell, including Lucifer and Hela, and many of the dead, like Zeus and Ares as well, making Mistress Death herself flee away from him.
After being turned down by Eternity, who explains connection between him and Chaos King that prevents them from directly fighting each other, Hercules and Cho manage to gather a new God Squad, which now includes them, Thor, Sersi, Venus, Daimon Hellstorm, Galactus, and Silver Surfer. Right in time to face Chaos King's assault on Earth.
Chaos King tricks Hercules into leading him to the dimension where all gods gather, from which he can attack and destroy all their realms, growing larger and stronger with every conquest. Amadeus Cho, to his terror, finds out he cannot think of any way to defeat him, before he and Hercules are lost in his very being.
The heroes get separated, and Thor faces the monstrous Glory, getting sent back to Earth as Donald Blake, without any memories. He then encounters Becca Steinhardt, a mortal who is still awake for some reason. Surfer, Hellstorm, Sersi and Venus ally themselves with Kami and Panther God of Wakanda to find a way to imprison Mikaboshi in Yomi, where he was trapped once before, only to find out Kami has been already enslaved by him and it was all a set-up.
Meanwhile, on Earth, the dead walk again. Great Beasts ally themselves with their mortal enemies, Alpha Flight – Sasquatch, Snowbird and their dead teammates, only to get stabbed in the back once the Flight finds out they wanted to take advantage of the situation and conquer the Earth. They are then killed by Chaos King.
Dead members of the Avengers face Grim Reaper, who has sworn loyalty to Chaos King for the promise that he may personally destroy the soul of every Avenger, dead or alive. Dead X-Men faces another of his servants, Raven God, who mission is to slay the eldest of Earth's gods.
Incredible Hulks, who weren't on Earth when all it's inhabitants fell asleep, find themselves allied with dead friends - Doc Samson, Glenn Talbot, Jarella and Hiroim - and racing against Chaos King's servants – Abomination and Zom – to find Rick Jones' wife, Marlo, who's carrying part of Death inside her – if Chaos King will gets her, he will use it to kill Death and destroy every soul on Earth.
Cho, Hercules and Galactus join the remaining gods in last enclave. Cho and Galactus go to Earth to transport all survivors into Continuum – an artificial Universe which Chaos King doesn't know about - but are attacked by his servants. Thor regains his memories, defeats Glory and solves Becca's mystery, to come back into the fight. Hercules faces Athena, who now serves Chaos King. When Chaos King absorbs the Earth, killing goddess Gaea, she uses her last power to make Hercules evolve and achieve true potential of his new powers. All-Father Hercules and Chaos King faces one another in the last, final battle, with the entirety of creation at stake. In final confrontation combined forces of heroes manages to seal Chaos King inside Continuum, where he can become what he once was without destroying real Universe, which already suffered critical damage.
Athena reveals that it was her plan from the beginning as now everything may be reborn from a scratch, better than before and with Hercules as supreme god ruling over it. Hercules rejects that vision and uses all of his power to restore the Universe to the condition it was before Chaos King started his attack. He also manages to bring back to life Zeus, Hera and all the members of Alpha Flight but he pays a heavy price, losing all his powers and becoming mortal man.
Soon after this event, Bruce Banner confronted Hercules and demanded that he fix the Hulks' problems as a reward for what they had done during the Chaos War. When Hercules revealed that he no longer possessed the All-Father's powers, Banner turned into the Hulk, stormed Olympus and challenged Zeus to a battle. The Hulk was defeated and chained to the mountain, where vultures devoured his body for days. Hercules and the rest of the Hulk family saved him. Zeus decided that Hulk had learned to respect him and he wouldn't pursue him any longer - such an auto-destructive persona as him will bring the best punishment upon himself.