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On one side of the Multiverse, Doctor Doom, Doctor Strange, and the Molecule Man were confronting the Beyonders. They demanded to know who dared stand before them, and Doom presented himself.
Meanwhile, on Earth-1610, Nick Fury was making the final arrangements for the upcoming and final incursion, and soon after sent all of S.H.I.E.L.D.'s fleet towards Earth-616. The fleet arrived to the incursion point, the Manhattan of Earth-616 and started firing at it. Numerous heroes tried to fend off the attackers. At the Baxter Building, Mister Fantastic was finishing getting ready the Future Foundation's Life Raft to be used to save a small portion of humanity. The Iron Man from Earth-1610 deployed the Iron Man Six weapon, but the tide of the battle is turned in favor of the heroes of the Marvel Universe when the Guardians of the Galaxy and Cyclops' Sentinels arrived to help. Other powerhouse heroes like Doc Green and She-Hulk arrived to Earth-1610 and stormed the Triskelion.
Once the Triskelion fell, the Maker deployed the Children of Tomorrow to attack. After the vessel transporting the Earth's "resurrection team" was destroyed by the Children, Mr. Fantastic was forced to put the life raft in action. As the life raft was deployed, Manifold teleported numerous heroes into it: Spider-Man, Star-Lord, Thor, Captain Marvel, and Cyclops, who had recently used a Phoenix Egg to become the Phoenix once more. The Cabal and the Maker were also able to create their own raft, with stolen designs from the original.
As Earth-616's life raft approached to the central point of the incursion, it suffered a hull breach, causing the portion containing the Richards family to drift away. The Invisible Woman tried to reconnect it to the rest of the structure, but failed, and it was destroyed. The rest of the life raft teleported away as the two universes collided and were destroyed.
Elsewhere, in another world, a gathering of alternate versions of Thor witnessed the ceremony held at Doomgard in which the Thor of Higher Avalon joined their ranks. The Thor Corps are a police force under the command of their God, Doctor Doom. Old Man Thor and the new Thor set out to do justice. Meanwhile, in the Kingdom of Utopolis, the Foundation discovered one of the life rafts, partially buried in the ground.
After retrieving Mister Sinister from the Bar Sinister, the Thors brought him to Castle Doom for trial. After being found guilty of allying himself with King Hyperion, the Baron of Utopolis, Sinister demanded his right of meeting his accuser in the arena. His accuser, Brian Braddock of Higher Avalon confronted Sinister and was defeated. Before Sinister could deliver the final blow, Doom stopped the fight. Doom confronted Braddock, who apparently had helped the Kingdom of Manhattan in planning to overthrown Doom. Jamie Braddock revealed himself to be the traitor, and he was sent to the Shield to be punished by being exiled to one of the deadliest domains of the world, the Deadlands. After the trial was held, Valeria von Doom informed Sheriff Stephen Strange about the Foundation's discovery, and that the readings from it concluded it would date from before the "beginning of time" (when Doom created this world). The Thors investigated the life raft, and from it emerged the Cabal, who immediately killed the Old Thor. When Thanos demanded one of the Moloids present in the scene to inform them of their location, the Moloid revealed they were in Battleworld.
Back to Castle Doom, Sheriff Strange was reading Emperor Doom a report of minor incidents that had occurred in Battleworld. The routine was interrupted by Doom, who dismissed the reports, and felt something was wrong with Stephen. Strange and Doom started discussing the nature of Battleworld and what was before it, when the Sheriff was interrupted by news from Doomgard. Sheriff Strange traveled to Utopolis, to investigate the life raft and the death of the Old Thor. After sending the Thor Corps to scout for the strangers, Strange revealed the existence of another person still inside the life raft, the Spider-Man of Earth-1610.
At one of the towers of Castle Doom, Sue Storm met with Emperor Doom, where Victor ultimately confessed he felt he was failing his duty as a god, he felt he wasn't capable of properly inspiring his people, and even though Battleworld is the perfect world he wanted, he considered himself its only flaw, which included the scars on his face, which he hadn't been able to cure. Sue repudiated Victor's claims and praised him, suggesting him that to create a stronger link with his people he should establish contact with them.
Strange brought Spider-Man and the Thor of Higher Avalon to his secret Sanctum Sanctorum, the hidden Isle of Agamotto, a place of remembrance for the lost world. Strange revealed he had found a vessel similar to the raft the Cabal had came from three years ago. Once it was opened, the survivors from the side of Earth-616 were revealed. Strange greeted the other inhabitants of his native universe, specially his fellow Illuminati, Black Panther and Mr. Fantastic. When questioned, Strange revealed eight years had passed since the last incursion, and the creation of Battleworld, a patchwork planet constructed with the remnants of incursion points between collapsing worlds, where nobody remembered their past lives.
In Utopolis, night had fallen and the Cabal had made a fire, and a few moments later, they were pinned down by the Thor Corps, and engaged with them in combat. Meanwhile, Sheriff Strange explained to the new-found survivors that when Doom and him confronted the Beyonders, they were able to kill them, and while Stephen didn't, Doom took their power for himself and used it to build Battleworld from the remains of the Multiverse. The hammer of the Thor from Higher Avalon started glowing, meaning he was being called for battle. Shortly after Doom was informed of the conflict against the Cabal, Strange and the heroes from Earth-616 stepped in and turned the tide of the battle in favor of the Thor Corps.
Doom remained unwilling to take part of the conflict until he saw Mr. Fantastic in the scene, he immediately teleported to Utopolis, and stopped the fray, demanding the newcomers to recognize his authority. Cyclops tried to best Doom, but was killed with little effort. To prevent Doom from prejudicially acting upon the interlopers, Stephen used his magic to teleport them away. Following the disappearance of the Cabal and the heroes from Earth-616, Doom confronted Strange for disobeying him, and ultimately killed him after Stephen accused him of being afraid of Richards.
The following day, a funeral was held for Stephen Strange in Doomstadt, with the cause of his death kept a secret by Doom himself. Once the dusk had fallen, Doom tasked Valeria to use the resources of the Foundation to find the interlopers who had been scattered across the world, denying to provide any more information than that. Once Valeria left, Doom opened a portal below a Molecule Man statue in his garden, walking down a set of stairs to meet the Molecule Man and informed him of Strange's death. The Molecule Man made remembrance of the day when he, Doom and Strange confronted the Beyonders. During Doom's mission to thwart the Beyonder's plan by killing Molecule Men across the universe, he also captured countless of them. When he confronted the Beyonders, Doom unleashed the Molecule Men's power to kill them, while the Molecule Man acted as a conduit to steal their power and give it to Doom. The Molecule Man finished his chat with Doom by informing him that with Strange's death, he had most likely started an unraveling that could take everyone down.
Back on Doomstadt, the Department of Science of the Foundation set out to find the interlopers. Jane Foster had infiltrated the Thor Corps, Black Panther and Namor found themselves in Egyptia, Captain Marvel had been captured by the forces of Bar Sinister, Black Swan had appeared in Doomstadt, Thanos was teleported to the other side of the Shield, and both Star-Lord and Miles Morales ended up in the Kingdom of Manhattan.
Three weeks later, Battleworld was in disarray, with disorder having escalated into open rebellion in several kigdoms, with somebody called "the Prophet" forming an army against Doom, Victor would later order some of his most loyal Barons to deal with the threat of the Prophet. Of the interlopers only Proxima Midnight and Corvus Glaive had been captured, while Black Swan offered help to Doom. While the Foundation were investigating, they found the source of Doom's power, and informed Valeria, who had become suspicious of her father, of this.
Somewhere in Battleworld, the two Reed Richards teamed up and started trying to find a way to defeat Doctor Doom, with Earth-616's Reed being unwilling to kill him, unlike his Earth-1610 counterpart. The Reeds had also started investigating the source of Doom's power, for which they sent both of the Spider-Men, Peter and Miles, to infiltrate Castle Doom using a device to guide them to said source, located under a statue of the Molecule Man. The Spider-Men encountered Valeria, who chose not to go with them due to her worry that, she would be not be capable of facing what would happen if she found the truth behind her father. In order to make the Spider-Men deserving of Valeria keeping her mouth shut about their presence in the Castle, she demanded to know if any of the people in the raft had killed Strange, and Peter confirmed Valeria's suspicions, that nobody from the raft was responsible. After opening a trapdoor under the statue, the Spider-Men delve into its depths and come across the Molecule Man. Owen questioned them if they had brought him something to eat, and Miles gave him a burger he had had in his pocket. After satisfying his hunger, Owen reveals that he's the battery behind Doom's power, at the arachid hero's request to find the source of Emperor Doom's power.
Meanwhile, Namor and Black Panther arrived to Strange's Hidden Isle of Agamotto, using the Key of Agamotto given to them by Strange, they entered, and after identifying themselves as member of the Illuminati to a projection of the deceased Sorcerer Supreme, they were given access to some powerful items Strange had collected over the years, including the Siege Courageous and an Infinity Gauntlet that worked only in Doomstadt.
Thanos, who had been captured by the Hel-Rangers, started talking to the sentient structure that formed the Shield, a giant alternate version of the Thing (Ben Grimm), and convinced him to reject Doom, and rise, causing the Shield to fall down.
The Prophet, who was revealed to be none other than Maximus, marched his troops forward to Castle Doom, where some of the most powerful Barons held the line. But betrayal was present during the assault, and Baron Sinister took the chance to turn against his fellow Baroness the Goblin Queen. Sinister was subsequently struck down by Baron Apocalypse. The expected reinforcements in the form of the Thor Corps joined the battle, but fighting against Doom's side, as Jane Foster had managed to convince the fellow Thors to fight against their god. Baron Maestro soon joined the battle with his army of Worldbreakers.
The two Reed Richards continued to plot from the distance, and they planned to use the fight in the steps of Castle Doom to infiltrate the building and steal "the most valuable thing that's left from the Multiverse" from Doom. Black Panther and Namor traveled to the Deadlands for reinforcements, and Black Panther used his title as the King of the Dead to convince the zombies to join the forces opposing Doom.
While the battle in Doomstadt waged on, the two Reed Richards were transported by Star-Lord to Castle Doom. The Thing from the Shield joined the brawl, and easily destroyed anything in his way. Franklin von Doom opposed him using his Galactus, and The Thing decided to surrender after learning the kid he was fighting was the son of Sue Storm. When God Emperor Doom joined the battle against the recently-arrived Annihilation Wave, Valeria convinced her mother to run away in order to show her something.
As the two Reeds looked for Doom's power source, Star-Lord remained behind repairing their ship, and he was confronted by Black Swan. The ensuing fight, during which Quill was easily overpowered, took the two of them to Doom's throne room, below Yggdrasill. Star-Lord used a splint of Groot on the magical tree, which engulfed it entirely, and turned Yggdrasill into a giant Groot that destroyed the castle from the inside out. Valeria and Sue witnessed the fall of their home from the castle gardner's, and they encountered the two Reeds trying to access to the Molecule Man's chamber.
Back in the battlefield, Thanos unsuccessfully confronted Doom, and was easily killed. In the moment right after that, the Siege Courageous opened up and a horde of zombies came out. After the zombies, Namor and Black Panther, who had the Infinity Gauntlet, came out proclaiming this to be the end of Doom's reign.
Doom tried to convince T'Challa and Namor to stop fighting by promising them to rebuild Wakanda and Atlantis, but they refused the offer and struck Doom down. Victor quickly regenerated from his own corpse and after dealing an energy blast at T'Challa and Namor which only killed the latter, continued fighting.
While Doom and Black Panther use their power against each other, Mister Fantastic and the Maker visited the Molecule Man. Owen once asked his visitors if they had brought him anything to eat, but they hadn't. The Maker quickly betrayed his counterpart and trapped him in a temporal bubble, claiming that he couldn't tolerate the kind of weakness Reed has shown. His plan is cut short as the Molecule Man sliced him and freed Mr. Fantastic.
Black Panther's battle against Doom came to an end after Victor crushed the Infinity Gauntlet. After subduing T'Challa, he realizes the fight had merely been a distraction. Doom quickly teleported to Molecule Man's stuatue and delved into his chamber, and tried to destroy Richards with a snap of his fingers. He was surprised when his power didn't work, and Molecule Man asked him if he had brought him something to eat, to which Doom replied he didn't. Thus, Owen claimed that Reed and Doom were in equal ground. Mister Fantastic and Doom engage in a furious combat, with Reed claiming that even though Victor did good, he could've done better, because he was too afraid of losing Battleworld he held it too tight. Doom accused Richards of believing he could've done better had he had Doom's power, and when Reed conceded he did, so did Doom. On the grounds that both agreed, Molecule Man gave his power to Reed, destroying Battleworld in the process. While the inhabitants were trying to outrun their imminent demise, Black Panther held tight to the Reality Gem of his Infinity Gauntlet as the world went white. When everything came back, T'Challa reappeared in the returned Marvel Universe.
Eight months later, Miles Morales appeared to be an inhabitant of the Marvel Universe instead of the destroyed Ultimate Universe. The young hero recalled when he and Peter Parker were leaving Molecule Man's chamber in Battleworld, and Owen had stated he owed Miles one for the burger.
In another side of the universe, the returned Future Foundation was created and charting the reborn Multiverse. Reed Richards used the Molecule Man's power to rebuilt realities with the help of Franklin Richards. Reed told Sue that he had learned that the difference between living and dying was managing fear, and not being so afraid of losing the things you loved that you held them too tight. Reed used to believe in entropy, but he now believed in expansion and resilience, in that everything lives.
Meanwhile, in Latveria, Doctor Doom had returned to his castle. He took off his mask and noticed his scars were gone, and proceeded to laugh.