In the midst of battle on a naval base, all Marvel Girl can think of is “what [she’d] give to be doing Calculus right now”, her most detested subject, and the only thing she was “worried about this summer”, until three weeks ago.
Jean arrived at Xavier’s School for Gifted Children, annoyed at her parents for “ship[ping]” her off to a “private school...with people more like [her]” and not letting her “finish out high school with [her] friends”. Her parents can’t bring themselves to describe her as a “mutant”, and are worried for her safety and of those around her when her telekinesis gets out of control.
She finds the door to the “big creepy mansion” unlocked and lets herself in. She meets Scott in uniform, who runs into her and knocks her to the ground, and displaces his glasses. Jean tries to break the awkwardness by cracking a flirtatious joke, but Scott is more anxious about finding his glasses. Jean helps him and he apologises, thanks her and continues running as if he is late. Jean is perplexed by Scott’s strange behaviour. She is then helped to her feet by Warren who shows her around.
Back to the present day battle on Cape Citadel Naval Base, Marvel Girl contacts Xavier to let him know that prior to the X-Men’s arrival, another mutant had infiltrated the base and “barricaded himself in the command center”. She questions Xavier’s judgement about sending teenagers into a live combat situation where someone can get injured. It is not the same as a virtual simulation in the Danger Room.
Three weeks ago, after a brief run in with Jean, Scott proceeds to the Danger Room to train with Xavier on the use of his optic blasts. Xavier sees his student making good progress and attempts to push Cyclops’ limits, but Cyclops is not ready to handle an unforeseen attack.
After the training session, Xavier tries to get Scott to talk about what’s “holding [him] back in there”. Scott explains when he gets overwhelmed, he is unable to “see the next move”. Xavier thinks there is more to it, and gets Scott to confess that he is afraid of losing control when he unleashes the full extent of his powers. Xavier encourages Scott to work on letting go of his fears because he sees Scott as capable of “leading the X-Men” one day.
In the present day on the naval base, Cyclops heeds his mentor’s advice on not being afraid to use his powers when the situation calls for it. And he blasts through Magneto’s barricade. But he gets hit and thrown off balance by the falling debris, and his blasts are accidentally misdirected at a nearby building, tearing a hole through the wall. Marvel Girl stops the falling building debris with her telekinesis and saves some officers from being buried alive.
Warren shows Jean around the school when she first arrives three weeks ago. Warren explains how Xavier had to telepathically coax his dad into enrolling him in Xavier’s school. Jean is “skeeved that [Xavier] brainwashed [their] parents” but Warren reassures her that Xavier has their best interests at heart.
The pair is interrupted by Hank bouncing off the walls running down the hall. He stops to introduce himself to Jean and Jean is impressed with his manner of speaking. Warren tells Jean that Hank is the “nicest guy in the world and crazy smart” but struggles with his less-than-normal physical appearance and strength. Hank leads them to the Danger Room and Jean comes face to face with the team prankster Bobby.
Bobby shows up for training wearing nothing but an ice cube in place of his “athletic underwear”. Bobby is embarrassed in front of Jean, irritated that his team mates conveniently forgot to let him know that “new girl was already in the house”. Warren takes his coat off and unstraps his wings. Jean is mesmerised, while Warren seemingly looks ashamed.
Back on the naval base, Xavier is communicating with Angel, who is the team’s aerial lookout. Angel reports to Xavier that he is seeing fighter jets without pilots being “thrown” into the sky.
Jean’s first encounter with the Danger Room was three weeks ago on her first day at Xavier’s School. She is witnessing the boys train when Xavier comes over to talk to her. Jean feels she is mislead by Xavier as she is “nuclear when and where the ‘school’ part happens” and where the “co-ed mutant fight club” comes into play. Xavier had to keep the combat training a secret from the parents. Their powers present a “unique challenge” that calls for a different approach to education. And while he strongly believes in a utopia where humans and mutants can co-exist, “creating it will be a battle” and that’s where the X-Men come in. Xavier is preparing them for the worst so they can protect themselves, and in keeping them away from their loved ones, protecting them as well.
Back on the naval base, the X-Men finally get to Magneto. When Cyclops hesitates in taking a given shot at Magneto point blank, Magneto tosses a desk at Cyclops and knocks him out. The rest of the X-Men come to Cyclops’ aid, and look on as Magneto steals a ship. Angel, Beast and Iceman start to chase after Magneto, but Marvel Girl admits defeat seeing that their team leader has fallen and they are no match for Magneto.
The X-Men return to the school to rest for the night. Except for Scott who is not taking the defeat well. After having his wounds bandaged he is back in the Danger Room training. Jean strolls through the halls. She passes a smiling Bobby, a determined Scott training, and Warren still hiding his wings. As she passes Xavier’s study, Xavier is seen conversing telepathically with Magneto. These friends have been divided due to their different beliefs.
The next day, Jean is outside reading when Warren speeds back to the mansion in his sports car. His dinner date went well until she wanted to get more intimate and Warren, afraid of exposing his wings, ran away. To cheer him up, Jean talks Warren into taking her to the carnival. Jean is clearly interested in Warren and hoped to have some fun alone with him. She is disappointed when Warren suggests to bring his buddies Hank and Bobby.
So she decides to invite Scott to join them as well, and finds him exactly where she thought to look for him: in the Danger Room training. Jean is almost hurt when she interrupts the training session. When he asks her nonchalantly what she wanted that she had to interrupt his session for, it upsets her that all Scott only cares about is training. She storms out.
At the carnival, Jean confides in Warren that only her parents know about her abilities, and it frightened everyone when her telekinesis manifested. But her parents still tried to be supportive. Warren on the other hand, had kept it a secret from everyone, which was surprisingly easy to do at boarding school for “the rich and narcissistic”. Being away from his parents meant that the topic of his wings “never came up”.
As Jean and Warren ride the Tilt-A-Whirl, Hank and Bobby are strolling around, with Bobby eating everything in sight. Hank theorises that “early mutants found refuge” in a travelling circus, “naming themselves freaks and sideshow oddities” in order to survive. They come across a stage performer who is evidently a mutant due to her appearance. Hank comes to defend her when prejudiced spectator ridicules her. When the stage security comes to break up the quarrel, the spectator punches him for being a mutant. Bobby starts a fight and a frightened woman in the crowd fires her gun in the air to get Bobby’s attention when she sees the mutants “winning” and the humans cowering in fear.
Meanwhile, Jean is trying to ask Warren out on a date when hear the gunshot. They rush over to the stage and see Hank and Bobby fighting a mob. Angel comes to the rescue of the stage performer and flies her to safety. Jean telekinetically retains some men in the air. Suddenly, the ground shakes and Fred brings an abrupt end to the fight. But he attacks the X-Men instead, whom he accuses of stirring trouble for them, mutants who aren’t able to pass for normal, and accept being labelled freaks by their “customers” because it is their “livelihood”.
Suddenly, a familiar red blast hits Fred. Cyclops and Xavier appear to “defuse the situation”. As a stop-gap measure, Xavier erases the memory of everyone at the carnival. Bobby wonders if they can help the mutants at the carnival, and Xavier hopes that they can.
Jean drifts back to her thoughts on hoping to date Warren when he walks over with Ginny, the girl whom he rescued. Jean sees Warren hitting it off with Ginny and he tells Jean that he’ll head back to the mansion later as he wants to fly Ginny around for awhile. Jean is disappointed when Warren turns her advances down again, and she barely acknowledges Scott when he comes over to apologise for what happened earlier and that he didn’t mean to be rude. Jean doesn’t feel like talking to Scott and wants to be left alone. A confused Fred returns to his trailer where Magneto is waiting for him.
Two weeks later, Xavier is having a talk with Jean about what’s troubling her because she’s changed since they returned from the Savage Land. Jean had previously been close friends with Warren, but he has noticed tension in their friendship as of late. And that Jean is having trouble working together and getting along with Scott, and that is compromising the team during training. Jean doesn’t feel compelled to discuss her private thoughts with Xavier as she recalls her trip to the Savage Land.
Two weeks ago, Marvel Girl and Angel spent two days “tied up on top of a mountain” in the Savage Land, a hidden land where dinosaurs still exist. Angel tries to make small talk to lighten the situation and unintentionally brings Ginny up. Marvel Girl snaps at him in frustration, scared that their lives are in danger and all he can talk about is his girlfriend. Angel is convinced that Cyclops, Beast and Iceman will be there to rescue them in no time, but a T-Rex shows up instead.
Jean is drawn out of her thoughts into the present day, where we see Bobby hurrying to Hank’s room, eager to tell him about the “gorgeous” brunette he saw meeting up with Magneto, Quicksilver, Blob and Toad, while waiting in line for lunch in the city. An exasperated Hank is interrupted in his work because Bobby can’t wait to tell him that he thinks he’s found the “Manhattan headquarters of the Brotherhood of Evil Mutants”. Hank is sceptical of Bobby’s “colourful details” but Bobby insists on proving it to Hank because “the only way Professor X believes [him] is with [Hank] backing [him] up”, and bribes him with lunch.
Down the hall, Scott is seeking Warren’s help with asking a girl out on a date. Warren dishes out some friendly advice from his experience. When Jean walks towards them and Warren catches Scott becoming awkward, he gets the hint that Scott is trying to ask Jean out, zests that Jean is not going to be susceptible to the usual tactics. Jean steals a coy glance at Scott as she walks away, her mind drifting back to the Savage Land.
Angel makes some suggestions to Marvel Girl about helping each other get away from the T-Rex. Marvel Girl is afraid of ripping Angel’s arms off when untying the ropes because she cannot control the focus of her telekinesis. But she is also not strong enough to lift and toss the T-Rex over the mountain. They decide to make a run for it.
Back in the present day, Bobby points out to Hank to the building across the street where he saw the Brotherhood gathered earlier in the day. Hank looks up and sees a billboard on a nearby building stating: “Mutant Menace! They could be anywhere”. Sighing, Hank knows this to be too conspicuous a hideout for mutants, until he spots Xavier approaching the very building Bobby had pointed out. Hank scales the building to spy inside the Brotherhood’s hideout.
Xavier had come to talk to Magneto. Despite being enemies, Magneto reprimands Blob for disrespecting Xavier and ushers him to his private chambers for a game of chess. Toad catches Hank spying in the window. Blob smashes through the wall and the Brotherhood chase down Hank onto the street.
Across the street, Bobby calls out to Hank, needing his help to save the life of a kid who has stepped into the path of an oncoming garbage truck. Bobby creates an ice ramp to slide the kid out of the truck’s way, and as the truck smashes the ice ramp, Hank catches the kid as he is flung off the ramp. Instead of being grateful, the kid pushes Hank away and calls him a “mutie freak”. Passersby start grabbing fallen trash from the truck and toss it at Hank. The Brotherhood stroll away and the police is called in as someone accuses of Hank and Bobby for causing a ruckus. Hank and Bobby disappear into an alley.
Bobby and Hank take separate trains back from the city. Bobby is worried that Hank has not returned that night and goes to ask to Jean if she has seen him. She had not and Xavier had been asking after Hank as well. Bobby is not used to being around girls and they talk awkwardly for a moment before Bobby returns to his room, leaving Jean to her thoughts.
Jean is still thinking about events in the Savage Land. After running for awhile, Marvel Girl and Angel try a new tactic: throwing sharp rocks at the T-Rex’s head. As Marvel Girl is finally getting some rocks to hit her target, she is knocked off her feet by the T-’Rex’s tail. As she is about to be eaten alive, Cyclops’ blasts the T-Rex unconscious. Angel is relieved that his team mates have arrived. Hank unties Marvel Girl and Angel. Marvel Girl walks over to Cyclops, embraces him and kisses him, in front of the team.
Three weeks have passed and Hank still has not returned. Bobby misses his best friend and is “taking it pretty hard”. As he wheels himself on his desk chair past the Danger Room, he sees Cyclops running a training session with a simulated team. Bobby runs in and pauses the session, feeling weird seeing a “fake” him having fun freezing “Nazi zombies”. Cyclops tries to explain that this is an exercise to help him be a better field commander. Bobby wants to participate because he is feeling bored and left out since Hank left and Jean treats him like “her annoying little brother”.
Outside, Jean is playing chess against Xavier, moving chess pieces the size of her with her telekinesis. Xavier wants to train her ability to multitask with her mental abilities and concentration. Suddenly, Hank returns to the school requesting to speak with Xavier. Jean is overjoyed at Hank’s return and forgets about the game of chess and the pieces fall on them.
Hank has returned to explain his resignation from the team in a “dignified” manner. He is tried of risking his life to protect the very humans who hate and fear mutants, and he won’t fight for Xavier’s cause anymore. Xavier refuses to respect Hank for giving up the hard fight. Hank calls Xavier out on sending them “out to die” at Magneto’s hand, and then act like old friends as if the battle was no big deal. That day that Hank spied on Xavier and Magneto in Manhattan upset Hank greatly, and he slams the door shut on Xavier.
Xavier, needing to explain his actions, does so to Jean who shared Hank’s sentiments but was too afraid to speak her mind. Xavier had known Magneto (as Erik) for a long time. Together they had envisioned a better world for mutantkind, but Erik, impatient and quick-tempered, lost hope in Xavier’s vision. Xavier knows Erik only wants what’s “best for mutantkind” and he refuses to give up on his best friend.
Seeing the falling out between Xavier and Erik made Jean realise that she had to repair her friendship with Warren, whom she had avoided talking to for the past month. She admits to having had a crush on him but since he wasn’t interested, she had moved on. Realising after the fact Jean was into him, Warren kisses Jean. Feeling insulted and angry, she leaves; their friendship still unmended. Warren then sees Scott in the hallway walk away annoyed, and now he has upset both friends.
Jean goes to visit Hank in the city. Hank wants to distance himself from the X-Men and focus on his life. Jean wanted to know why Hank quit the X-Men. All his life, Hank experienced being stereotyped and had accepted the social norm: ridiculed as a nerd for his smarts; after he manifested and gained extraordinary athletic prowess he became a popular jock; and when “people began to guess why he was hated for being a mutant. He thought that as an X-Man, he could be “the brain, the beast, the mutant”, and that the world would understand that mutants are so much more than their abilities or appearances. But instead, Xavier has the X-Men “dressed up like super heroes and punching things”, further cementing the notion in people that “mutants truly are different and scary”, and he can’t pretend that the world will stop hating mutants one day. And if he wants to “change the world”, he wants to use his intelligence and “not as a super hero”.
Jean concedes that this is a discussion for Hank to have with Xavier, but she walks away feeling more strongly than before that she’s not ready to give up on changing the world that hates and fears them.
The X-Men are once again sent on another mission. This time, Unus the Untouchable has robbed a bank and taken out “a S.W.A.T. team unarmed”. The X-Men soon find out that they are unable to touch him because of his force field. Marvel Girl is hurt when Cyclops’ blasts deflect off Unus and hit her instead. Angel is angered and disobeys Cyclops’ command to stand down, and charges at Unus. Cyclops stops Angel and the two start arguing. As Unus approaches them ready to attack, Iceman breaks up the argument and urges Cyclops to start putting his field leader training to good use and come up with a plan to defeat Unus. But Cyclops is out of ideas. Just then, Beast appears and blasts Unus with a strange device and saves the day. Marvel Girl is glad that she was able to talk Beast into returning to the team, but Iceman is still angry that his best friend quit.
Back at the mansion, Jean and Hank joins Scott for lunch. Jean tries to make small talk to ease the tension but Scott is disinterested. Warren walks into the kitchen with a peace offering of pizza, hoping to forget everything that’s happened and act like they’re friends again. Scott leaves, and so does Jean, leaving Warren to eat his pizza by himself with Hank’s company.
Cyclops goes back to the Danger Room to run a sentinels training session with his simulated team of Angel, Marvel Girl and Beast. Iceman who was supposed to join him in person is a no-show and Cyclops reluctantly calls for his avatar as well.
Meanwhile, Bobby is on the train heading back from the city. He was distracted talking to some girls on the train and missed his stop. He leaves Scott a message on his phone apologising for being late and begs him not to start “Sentinel Day” without him.
Something goes wrong during Cyclops’ session. The simulation stops and Cyclops’ is bombarded with ceiling tiles of the Danger Room. He is knocked to the floor and the tiles stack over him and form a dome-shaped prison. Cyclops calls out to Xavier in distress, but before Xavier can make his way to the Danger Room, he is captured by Magneto, and his telepathy is temporarily neutralised.
Jean is visiting Hank in his new laboratory set up in the basement of the school. She convinced Xavier that Hank needed “intellectual stimulation” outside of the normal curricular and Xavier agreed to turn the wine cellar into a lab for Hank. Magneto quickly captures Jean and Hank, as well as Warren. Bobby returns to witness his friends’ defeat at the hands of Magneto.
Magneto returns to Scott and has Jean imprisoned with him in the Danger Room. Magneto is going to force the X-Men into submission and join his cause.
Jean is unharmed but she is afraid that Magneto is going to kill him, seeing how he hurt Hank. Scott, thinking tactically about Magneto’s intentions, reassures her that Magneto was just showing off, either to “rattle” them or “impress” them into joining the Brotherhood. As Jean is more powerful than Hank, it was easier for Magneto to scare her by showing her how he could easily defeat her friend, playing off her “self-doubt”. Jean is impressed by Scott’s assessment of the situation, but Scott is beating himself up because he does not feel his leadership qualities are adequate.
Meanwhile, Magneto is having some trouble apprehending the youngest X-Men, Bobby. Bobby tricks Magneto with a statue and temporarily freezes him in a large ice block. Magneto summons every sharp metal object in the mansion to him to start chipping away at the block. Bobby makes a run for it.
Seeing as they are trapped in the Danger Room, Jean takes this private moment to clear the misunderstandings between her, Scott and Warren.
Jean: “We’re going to have this conversation right now because you have to get over this. But let me just say that this is the second time in like nine days I’ve had to tell a boy my secrets...and it is not heathy for a girl to have to spill her deepest darkest with that kind of regularity.”
Scott: “I don’t need your secrets. Believe it or not, I get it. Warren’s the kind of guy who gets the girl. It sucks, but it makes sense. I wish you hadn’t--”
Jean: “Wish I hadn’t what? You sound like an idiot right now. I couldn’t have expressed more interest with a billboard on the freeway. You’re the kind of guy who gets me. You’re smart and loyal. You don’t ever talk unless you have something to say. You’re the most dedicated guy I’ve ever met in my life. A life you’ve saved about a million times at this point. You’re my stupid hero, Scott.”
Scott: “What about Warren?”
Jean: “Warren...Warren is almost as dumb as you are. He kissed me because he misunderstood something I shouldn’t have told him. But it’s not Warren’s fault you never asked me out.”
Jean: “Yeah ‘Oh’. You know what, let me make this real easy for you. Yes Scott Summers, I will totally go out with you, but only if you blast us the hell out of this thing. Your X-Men are in trouble, Cyclops. It’s time to be the leader. Time to step up.”
And with that, Scott blasts them out of their dome prison, overcoming his greatest fear of losing control of his powers at full capacity.
Meanwhile, Bobby has found and rescued Hank, and the two best friends patch things up. They find Warren and release him from the tangled water pipes. The trio make their way to Xavier’s study where they find Scott and Jean already there and trying to free Xavier. Scott commands a task for each team mate without hesitation, and Warren is impressed with Scott’s newfound leadership. He credits Jean for boosting Scott’s confidence and apologises for his inappropriate actions.
But before they can free Xavier, Magneto blasts his way into the study and threatens Xavier’s life in front of the X-Men. Jean stands up to Magneto, telling him that they are not afraid of him. Xavier has trained them well and the X-Men are never going to give up fighting Magneto, and fighting for a better tomorrow.