The members of the Fantastic Four and Fantastic Force have found themselves caught in the middle of a battle between the Celestials and the Watchers, a conflict so massive in scale, they can hardly comprehend. From their vantage point on the fallen body of the Watcher known as "The One". Trying to get a sense of the situation, Sue tells her son Psi-Lord to try and read the minds of the aliens around them to find Uatu. Locating him, the two groups use Huntara's Psi-Scythe to teleport to Uatu's location. When the Watcher finally acknowledges their presence he tells them that he is aware of their concern over Aron the Rogue Watcher's plan but cannot interfere as he must witnesses the tableau unfolding before them. He explains that the Celestials have come to judge the Watchers to determine if they are a threat to the universe. Learning that the Watchers will do nothing to interfere with the proceedings, Psi-Lord attempts to pull the information they need out of Uatu's mind. After warding off the pain of the mind reading, Psi-Lord tells the heroes that Aron has set up a base between Mars and Jupiter. Having decided that the Celestials will destroy the entire universe he is planning on surviving the culling by creating his own pocket universe to escape it. The device that the Watcher provided them components to is the key to stopping Aron before it is too late.
With the current conflict between the Watchers and the Celestials too important to leave behind, Sue takes point and orders the two groups to slip up and tackle both problems at the same time. After transferring everything he knows into Sue's mind, Franklin joins Huntara, the Thing, Vibraxas, Ant-Man, and Kristoff Vernard through a portal to face Aron while the others stay behind. With the others gone, Sue, Johnny, Lyja, Devlor, and Nathaniel head towards Exitar the Executioner. Along the way Lyja imparts what the Skrulls know about the Celestials: that they are cosmic genetic engineers that may have had a hand in creating her race. She also tells them that none have ever seen what the Celestials look like under their armor and it is theorized that they actually exist in hyperspace, that their armor is actually allows them to interact with the physical world.
Meanwhile, within the temporal anomaly between Mars and Jupiter, Aron begins the final touches on his machine that will allow him to escape the destruction of the universe and create a new pocket universe completely under his control. Before he can finish, the Thing and his companions arrive on the scene. In order to keep the heroes occupied, Aron summons various Fantastic Four foes from different points in history to battle his foes. First comes Blastaar, then the Dragon Man, and the original Frightful Four, resulting in a full scale battle erupting. While back on the alien world, Johnny tries to get Exitar's attention wit a full power flame blast but it does little if anything. Sue and the others arrive on an invisible column to face him as well. When Sue questions how they can breach the Celestial's armor, Nathaniel reveals that Sue's invisible force powers actually tap into hyperspace and that since that is where the Celestials come from she can cause them harm. Concentrating as hard as possible, Sue unleashes the full force of her powers punching a hole through Exitar's armor. Back in Earth's solar system the heroes battle on against Red Ghost and his Super-Apes, Annihilus, Devos, as well as the Mole Man and his creatures. Among the battlers appears the Black Panther, much to the surprise of Vibraxis, but it is an earlier version of the Panther from prior to his meeting the Fantastic Four.
Back on the alien world, the other team have entered Exitar's body and find themselves in a strange alien circulatory system. As they venture deeper inside the massive alien being they are suddenly attacked by its immune system. Johnny and Lyja spring to action, fighting off the defenses so the others can continue on their path. Meanwhile, the Thing dispatches the Mole Man's creatures, and Huntara uses her scythe to send Devos away. Suddenly a younger version of Namor appears with an army of Atlanteans as well as the Awesome Android. To make matters worse, Kristoff points out that Aron is almost finished constructing his device. Back within the Celestial, Sue, Devlor, and Nathaniel come to a door barring their path. When Devlor fails to punch through it, Nathaniel's built in weapons blasts through it with general ease. As they continue onward, strange tentacles come out of the floor and ensnare the two men. Quick thinking Sue uses her invisible powers to lift herself off the floor and carry her away. The battle against the Aron continues on, and just as the heroes finish off Namor and his armies they are then attacked by the Silver Surfer -- from an era where he was still a herald of Galactus -- as well as Terrax, and -- much to Kristoff's surprise -- Doctor Doom. When Terrax tries to blast Kristoff, he is pushed to safety by Ant-Man. While Kristoff berates Lang for touching him their argument distracts them long enough for the arriving Occulus to destroy the weapon the Watcher had provided them, dashing all hopes of destroying Aron's device. However Ant-Man refuses to give up, even if it costs him his life.
At that moment within the Celestial body, Sue comes to a massive nerve center of pulsating energies. When she reaches out to touch it she is jolted by a bolt of energy that causes her to remember the fateful day when the cosmic ray storm and rocket crash led to the birth of the Fantastic Four. With the memories passed, Sue is shocked when a ball of energy emerges and takes on the form of her own body. The essence of Exitar congratulates Sue for making it this far. When Sue asks the Celestial what their purposes of threatening to destroy the universe, the god-like being tries to explain it to her as best as Sue can understand. It explains that after the Big Bang created the universe, the Watchers arose and began watching the universe, determined to merely observe following their disastrous interaction with the Procillians which ended in a nuclear holocaust. However, not all Watchers followed this strict edict. It goes on to explain that the Watchers have spent millennia downloading their knowledge into the massive Watcher known as "The One" in the hopes that it will survive the eventual end of the universe in what is known as the Big Crunch. However the Celestials had determined that in doing so, they have set the universe to expire before its time. When Sue asks why, the Celestial can only offer speculation, perhaps that they are wishing to start fresh and undo the damage they began when they inadvertently caused the destruction of the Procillians. As Sue mulls this all over, outside Arishem is about to make his supreme judgement in regards to the Watchers and the fate of the universe. The simulacrum of Sue tells her that the genetic code for destruction is being downloaded into Exitar to commit his ultimate act. Suddenly a beam of energy issues from Exitar's brow and strikes "The One", slaying him in a might blast of energy. While the threat is over with the death of "The One", Sue refuses to let the Celestials wipe out the rest of the Watchers, and so she uses her powers to attack Exitar's nerve center. The sudden attack causes Exitar's body to disintegrate, sending Sue and all those inside falling. However before they can suffer a fatal fall, they are teleported to safety by Uatu. Uatu explains that although the Fantastic Four have not stopped the Celestial's final judgement of the Watchers, they have delayed it by a few millennia. Realizing that the Watcher had manipulated them into helping his race, Sue demands that Uatu help them or else everything they have done will be in vein.
Back at Aron's hideout, the battle rages on with most of the heroes fighting off Gladiator, the Hate-Monger, Thundra, the Hulk and Ronan the Accusor. Aron gloats as his machine is complete and ready to activate. However before he can activate it, the machine breaks apart as Ant-Man, using his Pym Particles to grow to giant size, rips the machine to shreds. With his plans spoiled and his minions returned to their proper times, Aron curses the heroes for interfering with his plans. Suddenly, Sue and the others arrive with the Watcher in tow. Uatu vows to stop Aron once and for all, even at the risk of violating the oath that a Watcher shall not harm a member of his own kind. Aron and Uatu match powers but ultimately Uatu proves the better and he eradicates Aron from existence. In the aftermath of the battle the Watcher known as He Who Summons appears and finds Uatu guilty of killing a fellow Watcher. He then sentences Uatu to exile, stripping him of the title Watcher after mentally blasting Uatu, He Who Summons teleports away. The heroes rush to Uatu's side and Sue offers her sympathy, but Uatu believes that the punishment is just. Suddenly, Aron's artificial domain begins to shake. Realizing that it is coming apart, the former Watcher teleports all the heroes back to the Stealth-Hawk which is still on the Moon, much to the surprise of the man posing as Boris.
With the battle over and everyone but the Watcher accounted for, the heroes celebrate their victory. Nathaniel secretly muses on if the Watcher's citadel is unoccupied or not. In the aftermath of the battle, Sue has decided to accept the fact that Reed is probably dead and offers Ant-Man the opportunity to officially become a member of the team. Ant-Man is happy to accept, but Kristoff speaks up telling the group that he would be the better choice, a statement that leads to protest from both Johnny and Ben. While this is happening Devlor asks Sue what happened to Uatu and what he will do now that he is on his own. Sue tells him that she doesn't know but she believes that he is in a better place now and will turn out just fine.