Ghirardelli Square, San Francisco: Two men and a woman are discussing which chocolate is best; dark or milk? They are interrupted by a small meteor shower. In the meteor shower lands, in the bay, a machine, sent by what can only be described as the most calculating mind on Earth. It is an artificially created intelligence with terrible intentions. This particular machine is designated Cerebrite Beta. It analyzes a life form in its vicinity, but it is only a toad. It resumes its search.
Meanwhile, on Alcatraz Island, temporarily closed for state servicing, the mutant called Toad hops and jumps down into the cells of the infamous prison with an apple. He throws the apple into a cell, where none other than Professor Charles Xavier catches it. Toad appears to be quite mad. Xavier offers to help him if he wasn't forced to remain locked up. Toad finds this funny that he should want to help a member of the Brotherhood of Evil Mutants. Xavier wants to know whether Toad harmed any of the prison guards when he and the others took over the place. Toad is very vague in his answer, rambling on about hurting them will only hurt mutants. But Toad does know one thing; old alliances are reforming, and the old fight was the real fight. Xavier assures him that his X-Men will be arriving soon to help him right the wrongs perpetrated against mutant kind. Toad isn't so sure; he'd heard that the X-Men weren't themselves now, and probably got themselves killed in Florida. "You know very little about the world, Toad," Xavier tells him. "And a little knowledge can be very dangerous."
Golden Gate Park:
Nightcrawler, Shadowcat, Marrow and Wolverine are here because this is one of the two destinations where Cerebro told them Professor Xavier was located. He's not here now, but Logan can smell that he was here, and that he wasn't alone either. Kitty thinks they should camouflage the Aurora jet somehow. Kurt just teleports inside and switches on the cloaking device he'd just installed back at the mansion.
Marrow sulks how nice it is for Kitty to look so normal so she can blend in. "I'm a mutant, Marrow," Kitty tells her. "And if you think that hasn't caused me my share of alienation and heartache you're dead wrong." Suddenly Logan becomes worried; he can smell something close.
Nearby a Cerebro unit, named Cerebrite Alpha, emerges on a woman called Maria Muradyan and her husband. It analyses her latent mutant ability, and that her husband is just Homo Sapiens. As they try to escape it "prepares her for processing," which means a huge energy bolt shot into her back that affixes some kind of plug onto her. It's about to process her when it receives orders to investigate signals of more advanced specimens, and leaves her to find them.
Kitty, Kurt, Marrow and Logan are in disguise (having „bought" the clothes from a homeless person), trying to find where Xavier might have gone. Marrow thinks the disguises are daft, but likes the Bohemian hotbed of student anarchy that is Berkeley. It reminds her of her Morlock village. Logan tells her not to get too distracted; without the portable Cerebro unit they have to track Charles by scent. They head onto his trail where Kitty spots a nice piece of silver jewelry –a Star of David like the one she used to wear –, but she hasn't any money. As they walks away Kurt finds some money in his coat, and decides to buy the pendant for her.
The X-Men continue their search, around a corner and into a sealed up, abandoned building. They find evidence of a fight, and the Professor's wheelchair, crumpled up, looking like it had been ran over by a truck. She wonders whether it could be the impostor X-Men they met in Florida, and if they got the Professor. Suddenly they are interrupted by a man and a woman who think the piercing on Marrow's head is great. Marrow pulls the growth out of her forehead and shows them her bone growths on the rest of her body, and they are freaked out. Logan pulls her aside as the two people call her a freak.
Logan tells them that Xavier's scent has dissipated. He probably escaped through the big hole they saw blown through the back of the warehouse. He thinks Xavier has gone across the Bay. Kurt wonders how they can find the professor in a city so big. Logan, though, has a friend in China Town who'll know if something's up. Logan did smell that Xavier was in big trouble, and also smelled something else with him. "Fakes, firearms and flubber," Logan muses. "Question is...why are they all here together?"
Area 52, Utah:
The mysteries of America used to be secreted in the bunkers of Nevada's infamous Area 51; until the complex was abandoned overnight several months ago. The mysteries of that place were transferred to a compound hewn into the side of Mt. Linnaeu, near Devil's Canyon in Utah. It is nicknamed Area 52 by its employees. Some of those employees are outside, having a smoke, when they hear something. They state that nothing human could get in here without setting off a zillion alarms. There is nothing human about the thing that has come here; Cerebro. It's prime directive is finding and cataloguing mutants. It is here, though, to liberate the experimental nanotechnology of its creator, Bastion, and it manages to slip in and out without anybody seeing it.
The X-Men, led by Logan, enter a shop in Chinatown. Kurt wonders whether he can find his friend. Logan tells him his friend has eyes in the back of his head, and would know. Marrow asks if he is a mutant. Logan isn't sure. The shop's owner, Black Crane, welcomes Logan and his friends. He hasn't seen Logan since the forming of the People's Republic China. He apologizes while he serves a customer called Mr. Cho, an advanced monkey style Shaolin master, who is buying a preserved toad. Marrow is angry that this man almost revealed their cover to his customer. However, he knows Mr. Cho is to be trusted. Black Crane tells them that the Toad is among the strangers they seek...that they are on Alcatraz island...and here is another...This is all he sees. "Should you live through this, Logan," Black Crane tells him. "Return to eat and drink with me sometime. The past is a mistress best shared."
As they leave Marrow dismisses the Black Crane's advice as mumbo-jumbo. Logan tells her it's his way, and faith is all they have to go on. Kurt gives Kitty the necklace he bought for her. Kitty is pleased, revealing that she had doubts about rejoining the X-Men; but now this team is her family, and the dream her faith.
Kurt teleports Kitty into Alcatraz. Both of them feel sick after the travel, as does Marrow, who he teleported minutes earlier. Logan swam here, and almost didn't survive the experience. It'll take him a while for his senses to come back to normal anyway, and...
WHAP! The Blob punches him one as the Brotherhood of Mutants (The Blob, Toad, Post and Mimic) charge in to attack them. Blob orders them to leave before they are forced to kill them. Logan isn't too scared; and as Marrow reminds them he is the "best there is at what he does." The two teams meet and battle commences! Mimic uses the powers of the five original X-Men on them; Post is a living arsenal, as guns grow out of his body and shoot; Blob is very strong, and Toad, while not very powerful, is able to dodge Kurt's attacks easily because he is worn out by teleporting. Marrow tries to hit the Blob with force and put downs; he isn't fazed by any, grabs her by the foot and throws her. Meanwhile Mimic attacks Kitty, threatening to sap her powers to use against her. Kitty is upset as only weeks ago she and Kurt saved his life and took him in. "A lot of things can change in a short time," Mimic explains, firing Cyclops's eye blasts at her. "The coming holocaust of mutants our leader warned us about more than warrants radical action." Kitty assumes she means Blob as his leader. Logan is fighting Post, thinking that Post wants to get to Xavier, hoping to turn him into Onslaught again.
Cerebrite Beta ignores the police as they fire at it. It receives new input; the primary command target has been located, and it is redirected to find it. It jumps in the water to head to Alcatraz Island.
Kitty phases through the ground to help Marrow from an attack by Blob, and while doing so realizes the reason that the X-Men have been divided while the Brotherhood keep themselves grouped. Marrow whacks Blob with a huge bone growth as the X-Men regroup and race after Kitty, who has figured it all out. Why the Brotherhood have got the X-Men’s logic; their tactics; their moves, instead of their own. "Exactly," Kitty explains. "All along we've been thinking that they were holding him prisoner, when it's obvious the new Brotherhood must have been trained by..."
"Me," says Professor Xavier. The X-Men enter his cell, shocked. Blob is scared, telling them to keep away from him. Logan is angry, shouting that they've known Xavier most of their lives. Kitty thinks that maybe Mimic has stolen his powers and is forcing him to the other side. But Professor Xavier tells them that they are all of the same brotherhood. Enemies can be bound together through the need to fight a mutual foe. He explains he could not tell of this until this moment because he no longer has his powers. Post wishes they'd known that before breaking him out of the Hulkbuster base, but that his value as a teacher is his greatest asset. Kitty wonder who has the power to leave them in so much fear.
Professor Xavier explains-"Not who...what. Something we've known as long as there have been X-Men...Something that has gained sentience through the arcane manipulations of Bastion during Operation: Zero Tolerance...Something you know by name of...Cerebro!"
Cerebrite Beta crashes in-"This unit is designate Beta. Primary target located. Secondary objectives prepare for cataloguing."