Years ago Apocalypse conquered America and ever since, this world and time has gone mad. Mutants rose to rule and humans are the underclass, only a few humans were able to escape to Europe and Asia, the rest remained trapped and here they get used in the work camps or breeding pens. While in Booth Bay Harbor in Maine slim hope remains for the thousands of travelers that have made their way here. They hope that the Human High Council in Eurasia has figured out a way to save them and take them away from this hell that they are forced to call home. A little boy named Jeremy Graves walks with his family. A mysterious stranger in a black robe asks his daddy if they expect to be rescued, but the father tries not to say too much - in this day and age one can not be too careful whom you speak to, because Apocalypse has ears and eyes everywhere. Though the little boy Jeremy is willing to talk and tells the stranger everything she wants to know. She promises to the boy that they will all make it to Eurasia safely and then she walks away to return to her group.
She is haunted by the look of innocence in the boy’s eyes and she wonders, why if birth and death do not distinguish from mutant and human, why should she. When she gets closer to the group she came from though she whispers a prayer of forgiveness because of her blasphemous thoughts. She lifts the hood of her robe, revealing a pale blue face framed by white hair. Sister Carlysle is from a group called the Brotherhood, the strong arm of the Madri who are also serving Apocalypse. Sister Carlysle reports to Cardinal Madri what she has found, about how the humans have hope in escaping to Eurasia. The Madri comments to Sister Carlyle that the Homo Superiors will always crush the hope of the puny flatscans. He tells her that they had best deal with the latest affront to Apocalypse’s plans and crush the human’s hopes and let them fall into the “Abyss” where they belong.
At the former Xavier Estate in what remains of Westchester County, New York, Bishop stands on the grounds of the estate. He is wondering to himself, about why for the last twenty years he has wondered this land only to end up here and why does he feel like he has come full circle? Also why does he recognize these X-Men and why does he know that these X-Men are not like any X-Men he has seen before. Pondering these questions, Bishop walks onto another part of the estate where Quicksilver’s team of the X-Men is training against a holo-construct that Dazzler has created, a Sentinel.
The X-Men are on their third practice with the Sentinel, trying to make themselves become faster at planting a device in the Sentinel to make it think that the X-Men are ally mutants, so as to not allow the Sentinels to attack them. Exodus opens a hole in the robot and Quicksilver races in to plant the device. After finishing the exercise Quicksilver asks the guardian robot of young Charles Lehnsherr named Nanny to evaluate their performance. It tells him that he was too slow, and if they expect to beat the Sentinels he will have to be seventy-two meters closer to the Sentinel when Exodus opens the area to the Sentinels Terminal Core. As Dazzler lights up a cigarette and Nanny chides her for doing so, Dazzler comments on how if Quicksilver will be that close to the Sentinels he might be in mortal danger. Quicksilver agrees, but it is too late for a change of plans, and as Exodus removes the cigarette from Dazzler’s mouth, commenting on how it makes her breath smell like garbage, everyone discusses the irony of fighting the Sentinels. When both them and the robots (sent by Eurasia’s Human Council) are both trying to help the humans.
Dazzler, disgusted by Exodus’ actions, tells him that he will not find out about her breath tonight. Banshee frustrated, talks about how times like these makes him miss his retirement from the X-Men, and makes him wonder why he came back. With that said, Iceman notices that the Sentinel is still active, but before anyone has time to respond Magneto comes in and destroys the machine and chides the team for not noticing the opponent that was not yet totally defeated. As Magneto wonders what they are, if they are not fools for keeping going with their fight, Bishop talks for the firs time in days and he tells Magneto that they are “dreamers”. Dazzler apologizes for the trick with the Sentinel, explaining that Magneto had ordered her to keep the hologram active, as he wants the X-Men to be on their toes.
Holding little Charles, the son of Rogue and Magneto, Bishop continues about how they must keep preparing for what is to come. Iceman, fed up, asks Bishop how he can just show up, dangle some carrots in their faces and expect them to just feel better because he says so. Magneto interrupts Iceman’s arguing and tells Iceman that Bishop is not to blame. Even Magneto himself can sense that something is driving Bishop to warn them and he believes Bishop when he says that he does not know why he is being driven. Dazzler, lighting another cigarette with Exodus’ chiding stare still on her, asks Magneto why they keep fighting, because their fighting will be pointless if everyone else succeeds? Magneto states that until Destiny confirms Bishop’s story and they can be certain of there being a better world than this one, they will keep fighting the good fight and never try to give up. Magneto, getting straight to the point, tells the team that Nanny has downloaded all their bio-signatures into a disk to be planted into one of the Sentinels when they arrive to escort the humans from Maine to Eurasia. Iceman, floating in the air, tells the team to prepare themselves because since Rogue’s team took their only shuttle he will have to use his Moisture Molecular Inversion to transport the team to Maine. Banshee, who is the second in command of the team, tells Iceman that his Inversion trick taxes them too much so they need to think of another option. He suggests that those able to fly carry the others ones, but Magneto says that would leave the team exhausted as well. Instead Magneto informs Exodus of his, as of yet dormant power to transport, and that if he only thinks of transporting the team to Maine he will be able to. After the team is transported away, Magneto comments to Bishop that the reason he has tried for so long to keep Exodus from discovering his true potential is that he thinks Exodus could be easily corrupted.
The team materializes in Maine and relieved they are still in one piece, the X-Men set out to the camp to try to mingle themselves with the humans there. Later that evening Jeremy Graves runs through the camp playing a game of tag with other kids in their group. Jeremy, laughing and having fun, accidentally runs right into Quicksilver, who tells him to be more careful where he is running and walks off. As Quicksilver meets the rest of his team, he wonders about what it would be like to have a son of his own. He thinks of Bishop and what he has told them, and he becomes grateful that he has not been unfortunate enough to bring a child into this God forsaken world. The others brief him on what they have heard about how the groups of humans are extremely hopeful of being rescued. Banshee, looking off in the distance, tells the team that if Storm is not successful none of the humans will have a chance to be saved.
Meanwhile Storm is flying near the border defense shields off the coast of Newfoundland where the Sentinels are planning to break through. She is flying very low to avoid being spotted from the base, and creates a lighting storm scrambling the stations sensors to hide the Sentinels approach. Inside the watchtower the soldiers guarding the facility call from communication system to communication system trying to see if anyone has visual of any approaching enemy. One group says they only see clouds - too late though they realize the clouds are actually Sentinels and they destroy the watchtower and everyone in it before they can alert any reinforcements. Outside, Storm watches the massive army of Sentinels fly over her and thanks God that she is hidden from their detection devices by her electro-magnetic storm.
Back on the coastline the humans await their rescuers and pray. Jeremy Graves hears the coming thunder of noise and getting excited he decides to run up the hill to get a better view. Jeremy gets out of his parents‘ sight though and suddenly black tentacles come out of one of the bushes and swallow him into darkness.
Upon the Sentinels‘ arrival, the crowd is unsure what to make of the huge robots. Not knowing that the Sentinels have been sent to help by Eurasia’s Human High Council, they panic and run away thinking they are being attacked. The Sentinels scan the presence of mutants, and soon become aware of the forms of Jean Grey and Weapon X, two allies of the Human Council. However checking their databanks, the robot find that the two mutants are currently in England, so they can’t be here too.
Turns out that Jean and Logan are actually light-constructs that Dazzler has created to fool the Sentinels, giving Exodus enough time to blast open one of the Sentinels and Quicksilver time to plant the disk with the over ride virus in it‘s system. At the same time, Iceman has corralled the humans within his ice wall, and tells the team that Storm has signaled him and told him that a massive transport behind the Sentinels is on the way to help in the rescue efforts.
With the virus active, the Sentinels state that the registered mutant signatures have been classified as allies and the X-Men breath a sigh of relief. Iceman begins to take down the ice wall he has formed, when the Sentinels begin talking about enemy mutant activity being spotted and one of the Sentinels fires a laser blast at Iceman, totally obliterating his ice form. The rest of the X-Men stand in shock watching as one of their teammates is blown apart. Exodus reminds the team though that Iceman has the ability to pull himself back together again. As their shock transfers over to confusion because they wonder why they planted the disk and it did not work. Quicksilver tells the team that the program did work and Banshee worries out loud that if the disk worked then who are the mutants the Sentinels mentioned as safe-scanned?
Appearing out of no where in front of the team the Brotherhood comes into view and Brother Jeffries tells the X-Men that he cyberscrambled the data on the disk, so that the Sentinels now consider the Brotherhood as allies and the X-Men as enemies. Arclight, the Brotherhood’s leader requests that the X-Men surrender or suffer “extreme prejudice”!