After graduation, Scott and Jean have offered to help out the Institute by becoming instructors. Bobby, Ray and Jamie are trying to avoid all the classroom work. They even beg Wolverine to take over the class, so they can at least “go outside and break stuff”. Wolverine replies that “if Scott and Jean have something to teach [them], it might be a good idea to learn”.
Wolverine gets up and leaves when he detects a mysterious scent. He chases it into an alley, and is captured.
Back in the Institute, Scott and Jean start their first day of classes. Jean tries to convince Scott that “it should be exciting” to teach the new mutants “the science behind using their powers”, but Scott thinks that “they’ll rather be outside training”. Scott and Jean are greeted by a sight they were least expecting: a classroom in chaos. Cannonball bolts out the door, knocking Scott down on his back. Scott gives Jean an annoyed look: “Trust me, she says.”
Wolverine awakens in a cell, shackled to the floor. He finds himself in midair, and is promptly tossed overboard. He crashes into the wilderness below. Omega Red and Gauntlet jump out of the plane and proceed to track down Wolverine. Omega Red seeks revenge on Wolverine. X23 comes to Wolverine’s rescue. Apparently, Gauntlet used Wolverine to lure X23 out of hiding.
Scott and Jean find it harder than they thought it would be to control the class. The new mutants deliberately misbehave to get on Scott and Jean’s nerves. When Jean accidentally breaks Bobby’s stand-in statue, the rest of the class volunteer to go and find him, leaving Scott and Jean alone in the class. Scott’s devious smile reveals that he has a plan.
X23 tells Wolverine that she left the Institute that night because Hydra and S.H.I.E.L.D. are constantly on her tail and she did not want anyone else to get hurt. She tells Wolverine to leave her be, but Wolverine insists that he is prove she can fight through this. X23 walks into a trap on purpose, allowing Hydra to capture them both.
Viper leaves Wolverine to Omega Red’s disposal while she proceeds to mindwipe X23. Wolverine manages to evade Omega Red, and so does X23 the scientists. It is just as X23 had intended, to infiltrate the supreme headquarters of Hydra and destroy it. She tells Wolverine to leave immediately while she goes for Viper.
From a distance, Wolverine watches Viper’s craft explode. When S.H.I.E.L.D. comes to the aid of Wolverine, he covers up for X23, telling Fury “she didn't make it”.
In the Institute, with the class regrouped, Scott and Jean try again. They relate their personal experiences having been around in the Institute longer, and hope to share what they’ve learnt with the Professor with the rest of the class. To wrap up their little speech, Scott performs a trick shot with his optic blasts proving that Physics and Geometry do go hand in hand with their mutant abilities.