Early one morning, three students from Bayville High, wearing masks, trespass onto the property of the Xavier Institute to vandalize the area. Kitty and Kurt manage to scare them off before any trouble was caused.

Following the incident involving the Sentinels and the demolition of the Institute, Jubilee is being pulled out of the Institute by her parents, following Rahne.

While the younger students are having breakfast, Xavier calls a meeting with the older students, with news that they will be allowed to attend school “provided no one uses their powers”. A voting session will take place that night to decide whether a “permanent mutant ban” will be imposed. The students aren’t looking forward to going back to school, harbouring mixed feelings of fear, anger and rejection. Xavier tries to encourage them to show these people they have no reason to fear mutants.

Back at school, the X-Men are met with hostile behaviour and jeers from the rest of the school population. Kurt tries to blend in with the crowd as his true identity is not yet made known. Scott’s supposed girlfriend, Taryn, ignores him completely. Duncan decides that he will “overlook [Jean]’s problem” and they could put her powers to “good use” like cheating during exams. Seeing Duncan for what he really is, a “lughead”, Jean breaks up with Duncan there and then, grabs Scott by the hand and walks away. Scott and Jean share a nice moment hand-in-hand.

Principal Kelly eyes their return in disgust and invite the Brotherhood back to Bayville High. He plans to get the Brotherhood to stir up trouble so the parents and the board will vote to impose the mutant ban.

Back at school, Duncan and his gang take out their frustrations and hatred on Scott. Kitty and Rogue step in to defend their friend. Duncan loses interest and hightails. Kitty overhears Kurt lying about being a mutant and being friends with mutants.

While out riding, Logan catches sight of Colossus on the highway and gives chase. They come to an old abandoned farm. Both men engage in a tussle. Colossus tells Logan he is only here to deliver a message from Magneto: should Logan be tired of being persecuted, he is welcome to join the Acolytes. Logan dismisses that thought in a heartbeat. Seeing that Colossus is clearly troubled, Logan invites him to join the X-Men instead.

Meanwhile, Principal Kelly requests an audience with Duncan. He wants Duncan to band together with the Brotherhood and take down the X-Men. The Brotherhood show up at school and use their status as dangerous mutants to bully other students.

During a basketball training session, Jean is being accused of using her powers to perform an incredible tackle and scoring the ball. Jean denies the accusation, but even her own team mates refuse to stand up for her. The coach calls her to the bench and replaces her. Jean then spots Principal Kelly removing some sports trophies from the display shelves, among them, Jean’s soccer MVP award. He does not want the school to have anything to do with mutants and sees them as “cheats” and a “menace”, and everything but “normal”.

Xavier requests Jean to speak on behalf of the mutant student population. Outside the auditorium, Duncan and the Brotherhood approach the X-Men looking to cause trouble. While the Brotherhood have no qualms with using their powers, the X-Men try the best to abstain from using their powers while fighting back.

The parking area turns into a danger zone when Avalanche uses his powers to cause mayhem. The X-Men use their powers to save the others from harm, but they feared enough damage was caused.

The next morning, a solemn group of X-Men await as Xavier delivers to them the school board’s decision. The vote of acceptance shocked them, but they are none too happy about it either. Even still, Xavier encourages them not to give up the fight.