Mystique reveals her true form, and Scott demands to know how long and why she has been impersonating Xavier. As a fight is about to take place between the X-Men and the Brotherhood, the police and military arrive, with the intent of capturing all the mutants. With their powers giving them an edge, many of them soon escape and scatter in various directions. Scott had planned for all of them to meet back at Lookout Point after dark.
Meanwhile, the media is furiously churning out news reports on this event, arousing paranoia in the nation’s population.
At night, all of the mutants meet up as arranged. Unexpectedly, Nick Fury of S.H.I.E.L.D. turns up for their secret meeting. But he helps them out instead, giving them vital information to find their captured friends and team mates, stating he has his reasons. Storm and Mystique fight over leadership of the group, and not wanting to cause further complications, Storm reluctantly steps back.
As planned, Toad and Scarlet Witch go back to New York to find out if Magneto had perished, but it turns out that Quicksilver “performed a last minute rescue”. The rest of them head over to Area 51 to rescue all the captured mutants.
Shadowcat and Iceman make it into the main security controls, but due to Iceman’s foolishness, he dropped his pliers while fiddling with it, and set off all the alarms. While security is busy chasing the intruders, the captured mutants seize this chance to escape. Security is proving no match for the mutants and are taken out easily. As soon as all the captive mutants are freed and rejoin the rescue team, they make a run for it.
They climb up through an escape ladder leading to the roof as they are sealed in. Mystique being the last one out, Cyclops closes the hatch on her, demanding the whereabouts of Xavier in exchange for her freedom. Mystique refuses to answer him, and the rest leave without her, Jean having to stop Cyclops and Avalanche from “tearing each other apart”.
With the Institute destroyed and Xavier still missing, the X-Men go into hiding. Standing on a cliff overlooking the mansion, Cyclops is blaming himself for throwing away the opportunity of finding Xavier by leaving Mystique behind. Jean makes an attempt to comfort him. The X-Men ponder on their next move, “how to let the world know [they’re] the good guys, before it’s too late”.