Nightcrawler’s incredible solo effort has defeated the Marauders, and the X-Men hold all of them (save Sabertooth, who was swept away into the sewers) as prisoners. They decide to split up to conduct an interrogation. Rogue engages in a battle of wills with (that guy who disintegrates what he touches) threatening to use her power on him again. Iceman has a verbal struggle with Harpoon, as Harpoon claims that non-natives deserve nothing but exploitation and death in return for their ancestors’ conquest of America. Iceman attempts to point out the hypocrisy of this position. Nightcrawler alternates kindness and lurking menace on (that guy he was trying it on). But it is Wolverine who strikes a deal with Scalphunter, promising to introduce him to Wilson Fisk as a potential employee if he turns on Sinister. Recognizing the weakness of his negotiating position and having no particular loyalty to Sinister, Scalphunter agrees. He reveals the location of Sinister’s secret laboratory and offers his keycard. At Wolverine’s insistence, he has the earthquake-generating member of his team collapse the secret base Sinister has been constructing.
Unhappy with the deal but not trusting the district attorney’s office that the crime lord might well own, Nightcrawler dumps everything he has on Fisk on the desk of Matt Murdock. Due to the Worthington defense team’s investigation a year ago, Murdock is one of the few people in New York with no obvious connection to the X-Men that he is sure isn’t in Fisk’s pocket.
Based on the information they got from Scalphunter, the X-Men track Mister Sinister to his secret base beneath the State Home for Foundlings in Omaha. Bobby, the only one of the original X-Men present, is disturbed to realize this is the same orphanage where his friend Scott Summers grew up. That surely can’t be a coincidence.
They decide to call in assistance from the Brotherhood, and to Nightcrawler’s great distaste the one sent is Azazel due to his ability to arrive quickly and teleporting prowess. Using Scalphunter’s key card they take a secret elevator to levels beneath the orphanage. Azazel pushes Nightcrawler to test the limits of his teleportation ability, moving down the elevator shaft to locations he cannot see. Inside the lab at the bottom of the shaft, they confront Dr. Essex (Mr. Sinister as he is known to some) for the first time. His blueish, metallic skin speaks of his connection to Apocalypse.
Essex explains that he and Apocalypse wish for the same end but are pursuing it by different means, making them both allies and enemies. They are pursuing the Omega Point, a time of change when the entire world will be remade. Essex is following up on a breeding project that has been in existence since ancient times and whose modern product is Scott Summers and his brother is Alex Summers. Essex believes that by crossing their line with that of Jean Grey, the host of the Phoenix, he can produce the being who will bring about his promised salvation. Jean’s death seems to phase him not at all. He offhandedly offers to tell them where Apocalypse is so long as they do not bring Scott along. He believes that Apocalypse will destroy them all.
Frustrated and tired of dealing gently with monsters, the X-Men attack. Rogue steals some of Sinister’s power, and Wolverine literally cuts him in half. It seems to have little long term effect though, as Sinister transform into a liquid form and flees down the lab’s drain. His flight has eft them in possession of many of Essex’s scientific records and secrets, and they take them back to Hank McCoy for analysis. Hank is disturbed at their origin, but excited and tempted to learn so much about the secrets of life and the origins of mutant powers.
The X-Men ponder what to do next, asking Xavier for his opinion. He advises caution but is reticent about his own plans for dealing with Apocalypse. Then Ozymadius arrives with an invitation to have an audience with Apocalypse in Wakanda. He has heard they were seeking them as is willing to meet. Logan, Rogue, Iceman, and Nightcrawler travel to hear what the ancient evil has to say.
Apocalypse tells them that he has lived since ancient Egypt and has survived all who attempted to kill him since that time. His philosophy is of promoting conflict as a means of increasing the strength of the survivors. If you are strong enough to survive, you deserve to win. When asked why he cares, why it matters for him to try to make the world stronger, he explains he is the herald for the entity the X-Men know as the Phoenix. When life itself grows to a certain strength, the Omega Point will appear and the Phoenix will transform the Earth into a glorious new state that those on this side of the Omega Point cannot even imagine. The meaning of “Apocalypse” he tells the X-Men, is not doom or the end of the world. The name he has chosen means “Revelation”. He is the revealer of the way.
This all sounds like a big bucket of crazy to the X-Men. Apocalypse allows them to leave, but he warns them that if they do not serve him he will kill them. They know that they will need the most powerful mutants in the world if they hope to stop him. That means Magneto.
To free Magneto, but also to strike a blow against Apocalypse by doing the opposite of what he wants, the X-Men launch a campaign to warn the world about Apocalypse. They go on television and give newspaper interviews warning about the ancient mutant, detailing his methods, and attempting to unite the world against him. They ask that Magneto be freed to fight, and public opinion forces Nixon to agree. He releases Magneto to the X-Men’s custody, promising a pardon if Magneto can help defeat Apocalypse.
In the aftermath, Rogue asks Professor Xavier about the increasing jumble of memories she is accumulating. He explains that it is like mercury poisoning, where the more she uses her powers the more the toxic memories accumulate within her, slowly destroying her. When she asks for a solution, Xavier can only look helpless and advise her to use her powers as little as possible. Rogue’s powers are killing her, and there is nothing anyone can do about it.
As Bobby walks the streets are one night, Scott appears and confronts him. He has heard something of what happened in Sinister’s lab, the talk about the Summers bloodline and how the laboratory was underneath the orphanage where he grew up. When Bobby tells him the full story of what Sinister said and what Apocalypse said about the Phoenix, Scott is driven into a frenzy, He is tormented at the thought that his entire life, even his relationship with Jean, might be a manipulation. That the Phoenix Force might have survived somewhere. He reveals to Bobby that some of Jean’s Phoenix power still resides in him and has changed his powers, then disappears into the night. Bobby’s entreaties to stay and talk things out fall upon an empty street.