Everyone was shocked, and didn't know what to do; there was no one – not even Ben, not even Wolverine. Jean, Storm, Kitty, and Rogue were all looking angrily at Mystique.
Scott and Mystique face off, both enraged. Jean tries to probe Mystique's mind to find out where the Professor is, but somehow Mystique manages to block her.
Scott threatens her, and Mystique warns him that if he ever wants to see Xavier again, he needs to back off.
Their confrontation is interrupted by sirens; their group is quickly surrounded by police cars and helicopters.
The New Mutants are surrounded, but Ray blasts the cars and leads them off through the woods. Tabitha covers their escape by blowing up some trees. The Brotherhood take off in another direction, and Wanda covers their escape.
The X-Men are being targeted — several of them by name. They also demonstrate the general hysteria and fear running rampant among mutants.
The White House made a public announcement for everyone to not jump to any conclusions. The President of the United States said, "My fellow Americans, this is a time of gathering facts, not finger pointing, not turning against one another. As your president, I strongly advise you, above all, to stay calm."
The New Mutants follow Ray into the sewers where he says he knows of a place for them to hide. The X-Men regroup, but they aren't together long before the Brotherhood shows up as well.
"I don't know about this and nothing to do with Magneto's plan to expose them." Mystique explained them.
Jean bursts in, asking, "Why are you still here?" She doesn't know where Ben is or what happened to him.
Mystique said, "I want my team member back from the military, but I don't know where to start looking."
Nick Fury arrives there, he tells them, "I know where to start."
He hands over a disc, explaining, "On this disc, you'll find information on where the other prisoners are being held." Fury and his team then vanish just as quickly as they appeared.
Storm told everyone her decision, "We shall split into groups."
But before she finishes speaking, Mystique snatches the disc from her hand and declares, "I am in charge."
The Storm is furious; the sky darkens as lightning begins to flash everywhere.
Mystique warns her to back off, and Jean interrupts her to remind her that Mystique is still holding the Professor captive.
Mystique sends Todd and Wanda to New York to find out if Magneto is really dead.
Meanwhile, everyone watches as Jean boosts the velocity jet, which had been in custody, and the rest of them head off to the coordinates that Fury provided, which turn out to be Area 51 to rescue their teammates.
—
In New York, Wanda and Todd end up breaking into a news van and watch the footage that had been taped the previous day. In slow motion, they can see that Quicksilver rescued Magneto right before the building fell on top of him.
—
In the sewers, the New Mutants run into a mutant named Caliban. "Who are you?" he asks. "What are you doing here?"
Ray told them, "We're on the run and we're mutants just like you."
"Okay, you'll follow my lead then," Caliban agreed to save them.
—
At Area 51, Mystique morphs into a raven and sneaks in; she shuts down the fence sensors, and the others break in as well. Storm stands by in the Velocity for pick-up.
Inside, Wolverine is being questioned by the military while the others are standing nearby in clear plastic cells. Ben is still unconscious. The Blob is the last one being cut free from the green stasis goo.
Bobby and Kitty make their way to shut down the alarms. Mystique gets interrupted and doesn't turn off the motion sensors. Iceman creates a path across, but once Bobby cuts the wires, he twirls the cutter around his finger and drops it by accident.
Suddenly, troops are everywhere. Mystique tells Jean, Cyclops, and Avalanche to keep them back while she goes off with Nightcrawler to find the prisoners.
When the alarm goes off, the officer, who was questioning Logan, leaves to see what's going on.
And during the confusion, Spyke is able to pop a spike into Logan's restraint and free him.
Wolverine takes on the remaining troops, while Spyke frees the others. Blob is able to break free from the goo, and they round up all of the troops and get them contained.
Rogue picks up Ben in her arms, carrying him out as he's still unconscious. Nightcrawler and Mystique arrive a little later, and they all head off together to meet up with the others.
Security sealed off all exits, but they found Iceman and Shadowcat who were able to locate a hatch that led to the roof.
The Cyclops and Mystique are the last two through, and the Cyclops slams the gate in Mystique's face.
"Let me out!" Mystique screamed. "First tell me where the Professor is; otherwise, I'm leaving you." Scott replied.
Before she could tell him, she's cut off as Scott seals the exit and traps her inside. Avalanche goes after Cyclops, but Jean stops them and tells them there's no time; they have to leave now. Mystique is left behind as the others take off in the Velocity.
—
Later at the Brotherhood house, Todd sneaks in because police are watching the house. When he returns to the others, Lance is angry because he was supposed to get clothes for all of them, but he only got Wanda's.
—
Back at the Lookout, the X-Men discuss the loss of the Institute and Professor Xavier.
"Now what? The Institute is gone. The Professor is missing. We can't go back to school, and it's open season on mutants. At least Ben was saved..." Kitty was sad, looking at Ben. He still hadn't woken up.
Scott is upset that he didn't get the information about Xavier's location from Mystique, but Logan assures him that they will find him on their own.
Ororo tells them all that they have a new world to deal with now – one that fears them, and that somehow they have to find a way to teach them that they are the good guys… before it's too late.
Troops are swarming over the remains of the Institute. Reporters are present, and there is general anti-mutant propaganda on the news.
—
Rogue and Logan were shopping in a convenience store for food when more troops arrived and recognized Rogue.
A fight ensued, and Wolverine and Rogue managed to escape on Logan's motorcycle; however, the pursuing troops were close behind them.
—
A Congressional hearing on the "Mutant Menace" is being held at The White House, and Ororo and Hank show up to speak on behalf of the mutants.
Elsewhere, Juggernaut is "chased" off of a train by a security guard. Juggernaut tells him that he doesn't want to do it, but the guard doesn't listen, so he wrecks the train and leaves.
—
Nightcrawler, Shadowcat, and Iceman rig up a tiny handheld TV so that everyone can watch the hearings. Rogue and Logan come flying into the cave with the military right behind them. The X-Kids disable the helicopters without hurting anyone and take off in the X-Jet.
Meanwhile, a news van follows the police cars as they chase after Juggernaut. They come across a pile of wrecked cars and watch as Juggernaut heads for a huge dam.
Back at the hearing, news coverage of the Juggernaut's rampage is broadcasted. The Juggernaut is shown wrecking a tank, and the speaker declares that the mutants are all monsters. Ororo and Hank argue that they're not like that.
The X-Men finally arrive at the dam and go head to head with Juggernaut. Spyke topples a huge generator while Juggernaut is on top, and as he slides down the dam. Shadowcat jumps on top of him and phases him into the dam, leaving him partially trapped. Kurt ports in and out, releasing the locks on Juggernaut's helmet.
Cyclops takes off his visor and blasts him full-force with his beams, knocking the helmet off of his head. Shadowcat and Rogue phase up behind him; Kitty boosts Rogue up onto his shoulders.
Rogue continues to absorb his powers. Juggernaut rises to his feet first and goes after the Rogue. They go head to head, but Juggernaut can't touch Rogue. She lifts him up over her head and throws him off the top of the dam. In mid-flight, Iceman freezes him into a huge block of ice. Then they lose track of him.
Back at the hearing, where they've just witnessed the X-Men versus Juggernaut fight.
The speaker is shocked and asks "What did they do?"
Ororo tells him that they've done what they were trained to do, to use their powers for good.
On the dam, Rogue tells them that she just absorbed a huge portion of Juggernaut's mind. She now knows where the Professor is. The X-Men find Xavier locked up in Juggernaut's holding tank at the Stokes County Maximum Security Facility. Wolverine shows up and tells Cyclops that he did a good job.
Later, the President gives a speech, "My fellow Americans, human and mutant — I stand before you now to clear the X-Men of any wrongdoing in the giant Sentinel robot disaster. The real criminal mastermind, Bolivar Trask, has been arrested and charged. We need to be open-minded. And we need to give this mutant question more time."