The X-Men
Part 4: The Culling
While their friends are undergoing all these missions, the X-Men do not stand idly by. Not entirely convinced of Bishop’s story, they continue with their regular activities. Even if this world isn’t the true reality, it’s stilltheir world and they will fight for it until they die. Receiving news of Apocalypse’s son Holocaust having started another culling in Chicago, Rogue takes a squad of X-Men with her to oppose him and rescue as many humans as they can. Despite it being a suicide run, Sabretooth, Wild Child, Sunfire, Blink and Morph come along, as they all feel very strongly about Holocaust and the cullings. Once they reach Chicago, the X-Men try to calm the panicking humans, but soon Rogue looses control of her squad. At first Sunfire goes ballistic, as he remembers similar events having happened in his native Japan, with him being the sole survivor. Next, Sabretooth decides to settle an old score by taking the fight to Holocaust himself. Against Rogue’s orders, he takes Wild Child with him, abandoning the rest of the team.
The two X-Men find Holocaust in Indianapolis, where the newest Infinite processing plan is located. Although his intellect is somewhat limited, Creed sends Wild Child back to the Rogue’s team with this valuable piece of information, while he dukes it out with Holocaust. Although Sabretooth manages to crack his bio-containment suit, Holocaust is the last one standing, and further tortures him, before chaining him to a rack rock slab with his chest ripped open. Wild Child makes it back to Chicago with the Infinites hot in pursuit. The X-Men save him and, as he has no other way to communicate, Kyle licks Rogue’s face so that she absorbs the knowledge from him. Immediately, the team rushes to the processing plant but, when Blink sees the ravaged body of her mentor, she freaks out and takes on Holocaust by herself.
The villain laughs at the girl’s effort, though he underestimates her. She not only destroys major parts of the building but also, with some tricky maneuvering, is able to best him. Bested, Holocaust ends up falling into a tank of genetic goo. However, Holocaust survives even this and returns, now madder than ever. Rogue and Morph come to Blink’s aid while Sunfire and Kyle continue to evacuate the plant’s prisoners. Right before Holocaust is defeated, he activates a teleportation platform and escapes to his father’s stronghold on top of the ruins of Manhattan. [Astonishing X-Men (1st series) #1-4]
Part 5: The Evacuation
The other half of the X-Men – Storm, Banshee, Exodus, Dazzler and Iceman, led by Quicksilver, travel to Booth Bay Harbor in Maine to help the many human refugees that are hoping to be rescued by the Sentinels of the Eurasian Human High Council. Storm ensures that the approaching robots aren’t detected by Apocalypse’s seawall by causing static interference with a lightning storm. But the X-Men still face one big problem; in the eyes of the Sentinels every mutant is an enemy. As a result, the two parties that have come to help the humans would end up fighting each other. To prevent this from happening, the X-Men have come up with a override virus, which they need to plant into one of the Sentinels. As if this procedure is not already hard enough, the team are further disturbed by the Brotherhood, who have been sent by Apocalypse to stop the humans’ escape and also the newest Horseman, Abyss, who enjoys abducting some of the refugees and sending them into his inner void of darkness.
Using teamwork, the X-Men are able to overcome the Brotherhood. Only Box and Copycat escape by hiding among the refugees and letting themselves be evacuated with them. The team is finally able to proceed with their mission, though by threatening the hostages’ lives, Abyss blackmails Quicksilver into dueling him. Realizing that she is falling in love with Pietro, Storm accompanies him to the site of the battle. Surprisingly, he manages to defeat Abyss by wrapping him up in his own coils but he is sucked inside his own void. [Amazing X-Men (1st series) #1-2]
Part 6: The Kidnapping
While his X-Men are busy fighting for their world, their leader, Magneto, stays behind at the mansion in Westchester, along with Bishop. 
At first, the time-traveler accuses Magneto of being a coward as he lets hisfollowers go into battle without him. Magneto explains that, if they succeed and the timeline gets restored, baby Charles, the infant son of he and Rogue, will no longer exist and he wishes to spend one last night with him. Suddenly, alarms go off, as the estate is being invaded – Apocalypse has finally discovered the X-Men’s hideout. Nanny immediately wraps the baby in a cocoon of omnium steel and takes him to safety in the old Morlock tunnels, mere seconds before the Infinites attack. At first, Bishop and Magneto manages to keep them at bay, however they are only cannon fodder. Their actual opponent is Apocalypse himself and he easily knocks them out. Magneto tries to cause an explosion that will kill both Apocalypse and himself, but stops the device when he learns that the Vanisher was sent after Nanny and baby Charles. Little does he know that Nanny has already terminated her pursuer.
Finally, both men are rendered unconscious and carried away by Apocalypse’s forces. While Magneto is brought to Apocalypse’s stronghold, Bishop is taken to a secret base in Quebec for interrogation. There, he is tortured by the Madri and the Shadow King, who learns from the images in his mind that Bishop is from another reality. Before he can probe any further, Bishop is able to force the Shadow King out of his head. However, Abyss re-materializes and intends to finish the job the Shadow King started. Though he does not exactly understand what it is the X-Men are hoping to achieve, most likely it will be no good for Apocalypse, so it needs to be prevented, even if that means killing Bishop.
Part 7: The Reunion
When Quicksilver’s team of X-Men returns to the mansion, they discover evidence of the recent battle and also learn that Bishop and Magneto have been brought to different locations. Iceman departs to fill Rogue’s team in on the bad news, while Exodus and Dazzler are sent to search for the robot and the baby she is guarding. Knowing that Bishop is crucial to their plan, Quicksilver makes a hard choice and decides that he, Storm and Banshee will try to rescue him, even though it might mean the death of Magneto.
Once they reach Quebec, Storm rushes to Bishop’s aid, who is about to be killed by the Madri, while Quicksilver and Banshee more or less by accident discover the one, true Jamie Madrox, held in a cell. To their surprise, he doesn’t fight them, but asks to be killed as this would leave the Madri soulless shells. The two X-Men do not want to kill an innocent victim, and wonder what to do as Abyss appears out of the shadows. He taunts them and starts a fight and, sacrificing his own life, Banshee flies into the void within Abyss to tear him apart with his sonic scream at full force. Quicksilver grabs Jamie and manages to outrun the resulting shockwave, though Madrox repeats that he needs to die for the sake of Storm and Bishop, who are about to be defeated. Jamie shuts the dupes off but the process strains him so much that he too dies.
By the time that Storm, Quicksilver and Bishop return to Westchester, they find the other X-Teams waiting for them. Colossus and Shadowcat successfully retrieved little Illyana though at the cost of their charges in Generation Next and Nightcrawler convinced Destiny to come along as per Magneto’s request. In the sewers beneath the mansion, Dazzler and Exodus find the remaining X-Ternals who inform the others that the M’Kraan Crystal shard and baby Charles were stolen by Guido, who betrayed their team. After some deliberation, the heroes prepare themselves for their last strike against Apocalypse. For the plan to work, they need that M’Kraan crystal shard, and if they already have to break into the stronghold to get it, they can also try to save Magneto and baby Charles at the same time. [Amazing X-Men (1st series) #3-4]