Wolverine and Cyclops rescue a mutant in Sydney. He was hunted by a Sentinel but the two X-Men quickly destroy the robot.
A mysterious woman called Ms. Nova is showing Bolivar Trask's nephew what happened thirty thousand years earlier. Thanks to a virtual simulation she shows him when homo sapiens ancestors brutally took the land from their predecessor's. He sees the horrors for himself and he is told that within four generations mutants will have done the same to humans unless they act now to extinguish the mutant germ.
Meanwhile at the Xavier Institute Professor Xavier is about to test the new Cerebra machine that the Beast has built. Xavier is sat inside the giant elliptical device that will magnify his senses to the tenth power. Jean telekinetically lifts them something to drink, as she speaks to the Beast about his further mutated appearance that is believed to be related to this year's mutant baby boom. They turn their attention to the professor as Cerebra is switched on. Cerebra creates an image display of the world with lots of peaks where the mutant gene can be found. They comment on the large number of mutants appearing when suddenly they see a large spike in Ecuador, South America. Xavier cannot tell what it is so they decide to get Wolverine and Cyclops to check it out on the way back from Australia.
In the X-Wing Wolverine and Cyclops are talking with their new passenger, Ugly John, whom they've just rescued from the Sentinels. Whilst they are talking, Wolverine's healing factor is repairing his damaged tissue after he was set on fire by the mutant hunting robots. Ugly john passes out and Xavier mentally contacts them.
Meanwhile Mr. Trask is physically sick after seeing the simulation, after all he is only a mere dentists, unlike his late uncle the anthropologist Bolivar Trask. Ms. Nova leads him from their helicopter to a valley where a second, so far unknown Master Mold artificial intelligence factory unit had been built years ago. Ms. Nova´reveals that this unit was designed to adapt to its surroundings and rebuild with any technology it finds, but it was forgotten about as the area was in the middle of some rebel wars.
In a telepathic conference call, the X-Men are sat on a couch talking with the professor. He tells them that the school is back open from Monday to help all the new mutants that are being born. They talk about the new uniforms and then Scott tells the professor that they'll stop off at Ecuador. Wolverine comments to Cyclops about wanting to get out of Xavier's head quickly, however Cyclops says he doesn't know what he is talking about, even though the tension between him and Jean was obvious.
Back at the mansion Beast and Jean are getting familiar with the new upgrade to the Beast's lab that has a tele-immersive display. Hank comments on the atmosphere between Jean and Scott, but Jean tells him not to talk about it. They comment on the motivation of the professor and the amount of money he is spending when all of a sudden jean feels something strange. She heads back to Cerebra.
Professor Xavier is about to get out of the device when all of a sudden he hears a voice in his head. The voice tells him that it is going to take over him and make him a murderer. Xavier is struggling to fight for control and his nose starts bleeding, nearby a drink explodes. He pulls out a gun, points it to his head and informs the voice that he'll shoot if they don't leave. Jean arrives and detaches Xavier from Cerebra. Xavier is barely conscious and babbles to Jean to warn everyone in Ecuador.
Back in Ecuador, Ms. Nova wipes some blood from her nose and apologises for being "miles away". Mr. Trask is complaining about the journey and asks why she has taken him to this place. Ms. Nova guides them to a clearing where a group of dead soldiers are lined up. A noise is heard from behind them, and suddenly the troops are cut to pieces. Ms. Nova tells Mr. Trask to look at and talk to humanity's last hope. He panics and shouts for them to stop. The Wild Sentinels recognise the voice as Trask and stop in their tracks. Ms. Nova removes her hat to reveal a bald head, her face is very similar to Xavier's, and they head into the Master Mold factory followed by the Sentinels, who seem to be modelled after various jungle life forms.
Summary written by : Dean Clayton