A man is seen waiting inside his large exclusive private school. Suddenly, he "calls out" mentally to his students stating that he is Professor X and he is ordering them to appear in class at once. Then four costume-clad people appear and report for their lessons: Cyclops, the Angel, Iceman and the Beast. Angel and Cyclops help the professor get comfortable in his chair. Iceman plays a prank on Beast and freezes his arm. Angel has to pull the two off each other and Professor X begins their training lessons using his "training machine".

The Beast is first and is given timed lessons to help him with his agility skills. He first grabs a taut wire with his toes in a second and a half. He then spins wildly on the wire and jumps through the room in exactly three seconds. Then he practices his balancing skills while Cyclops slackens the wire tension causing him to jump off and land on his feet. The Angel takes his turn and tests out his wing reflexes. He flies around jet flames, through a giant closing clamp and then skips through a bladed spinner without a slip. He becomes overconfident and when a sound concussion blasts around him, he loses his edge and begins to fall but then recovers. Iceman asks the professor to allow him to take more risks even though he is the youngest student. The professor tells him not to rush things. Iceman then feels that if he is going to be treated like a kid, then he will start acting like one. He finds "snowman items" and puts them on to joke around. Beast throws a ball at him since he is off-guard and Iceman reacts quickly creating an ice "boomerang-sled" sending the ball right back at Beast. Cyclops shows off his leadership skills and uses his beams to stop the group from goofing off. Professor X stops the team and readies them for the new student who has just arrived by taxi.

A redheaded woman steps from the cab and the group begins bantering with each other about the fact that a girl is joining the school. The team goes and changes while the woman enters and is greeted by Professor X who apparently sent her [Jean Grey] a letter to be enrolled as a student of his school. She questions the type of school that she sees and Professor X states that it is a school for the "specially gifted", mutants, like herself and the others. The professor introduces the rest of the team, using their real names and codenames, to Jean Grey, whom he says is now known as Marvel Girl. She shows off her powers of telekinesis to the rest of the team by moving chairs and books. The Beast, tries to give her a kiss and she turns him upside-down and spins him wildly in the air then throws him onto the couch. Professor X then tells the group their mission is to protect the world from mutants who would harm humans or other mutants.

Meanwhile, just such a mutant named Magneto, is hiding near Cape Citadel watching a missile launch. He uses his powers of magnetism to control the missile and send it crashing off-course into the nearby waters. The Army and NASA standby and are astounded that the missile was destroyed. They conclude that someone tampered with the missile prior to launch. The next day, the Daily Globe newspaper states that this was the sixth missile to be destroyed and a "phantom saboteur" has struck again. Then the soldiers begin seeing weapons firing randomly and tanks being controlled remotely. A message suddenly is written out in metallic dust in the sky and reads, "Surrender the base or I'll take it by force. - Magneto." While the message is being read by the soldiers, Magneto launches a missile from a silo near the base. He causes it to fall into the sea near an unmanned target ship. Magneto then walks into the base and takes control of it. He uses his powers to entrap the soldiers in a "magnetic-fence" from which they cannot escape.

The X-Men are alerted to the crisis at the Cape. They each get ready into their uniforms and ready to go. They are driven to the airport in Professor X's Rolls Royce and take his private jet to the Cape. The X-Men arrive and request the army hold off firing on the base for fifteen minutes. Cyclops uses his power to make a hole in Magneto's magnetic force field and this alerts Magneto of their presence on the base. Magneto fires heat-seeking hunter missiles at the team. Angel causes the missiles to lock onto him and follow him around in the air, while Iceman freezes them with snowballs. One missile gets through and Beast catches it with his feet. Marvel Girl then telekinetically sends it off into the sea. Magneto is amazed at the team's abilities and sends a pile of metal hurtling at Angel. The team stops to help him, while Magneto rolls a flaming barrel of rocket fuel at them. Iceman quickly encases the team in an ice cocoon when suddenly the tank blows up.

Magneto thinks he has won and starts to walk off when suddenly Cyclops' beam shoots out from the ground. The team emerges and begins to strike at Magneto full force. Magneto takes flight via magnetic repulsion and blocks the team from following him with a magnetic force field. They eventually breach it and Magneto has already disappeared. The army is gracious that the base is safe once again and thanks the X-Men for their help. The team then flies back home in the jet, while Professor X telepathically congratulates the team for a job well don