The Sentinels test so far have yielded success in taking out and capturing Wolverine. Trask and his scientists intend to do more tests.
Meanwhile back at the Institute, the trapped new recruits are trying to look for a way out now that the mansion’s security system has turned against them. Outside, Scott, Amara and Tabitha are trying to force their way back into the mansion via the X-Jet’s launch pad, but it seems virtually impossible without the aid of Jean’s telekinesis. Scott improvises and asks Amara to melt their way through the cliff face instead.
At the dock, the X-Men and the Brotherhood are stumped by the disappearance of Magneto and the Acolytes. Searching the warehouses came up negative, until Gambit’s charged card turns up in the presence of one of the groups. As everyone dashes into battle, Quicksilver speeds off in a different direction, cementing Scarlet Witch’s suspicion that they have all been set up. The Acolytes reveal themselves and attack the X-Men and the Brotherhood. As the teams do battle, Scarlet Witch searches frantically for signs of Quicksilver and Magneto.
Returning to the Institute, Scott shows up just in time to stop Berzerker from “frying” the security controls. Overrides fail, and with sixteen seconds left, they have to find a shelter before the whole mansion blows up.
While reviewing the damages Wolverine caused to the Sentinels, one of Trask’s officers discovers the battle going on down at the dock. Trask demands the Sentinels to be put into action immediately.
Surprisingly, the X-Men and the Brotherhood are working well to take out the Acolytes. Just as Scarlet Witch and Storm spot Magneto, he destroys the foundation of the dock, causing the ground to collapse beneath the feet of the mutants. Scarlet Witch manages to cling onto the edge, but Magneto flings her back into the ditch.
Unfortunately for the X-Men, they caved right into Trask’s hands. The Sentinels are quickly dispatched. Magneto sends his Acolytes away and raises the Sentinels and the fallen mutants up into broad daylight, exposing them to the entire world as the battle is caught on tape by the news crews. As the mutants fight for their lives, they are slowly taken out by the Sentinels and imprisoned in a green substance.
While Magneto is enjoying watching the mutants being taken out by the Sentinels and using his powers to hold by the Marines, he exposes himself to a Sentinel scan. Scarlet Witch finds him first and hexes his powers, rendering him helpless to a Sentinel attack. Xavier takes out the Sentinel, which falls onto Magneto, possibly killing him in the process. Xavier calls for a retreat, and that they’ll have to come back for the others later.
Returning to the Institute the X-Men are devastated to find their home destroyed. Jean is the first to rush out of the X-Copter to survey the damage. Luckily the new recruits, though scathed, are unharmed. Seeing they have returned, Scott steps ahead of the group in firm, quick strides. Jean runs towards Scott and greets him in a tight embrace. Stone cold, Scott wordlessly detaches himself from Jean.
Scott approaches Xavier, grabs him by his jacket and lifts him off his wheelchair. Scott accuses Xavier of all the damage that has happened and tosses him to the ground. Scott is restrained by Bobby and Kurt. Xavier turns to them and laughs evilly, and crawls up from the ground, revealing herself to be Mystique, stating that “things are about to get much worse”.
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