The X-Factor is the 17th episode of the second season.
Tony’s new friend Annie Claremont turns out to be a mutant on the run from Magneto, who wants to use her to assassinate Senator Robert Kelly, an anti-mutant politician. Iron Man tries to protect her, but how can he fight a mutant with a mastery over all things metal?
Tony in his armor, is investigating magnetic fluctuation in the infrastructure of the subway and sees that it is spiking in the area he is in. His HUD and communications aren't functioning, causing him to look around with the ARC light. He finds Simon Trask tied up in a corner of the room unconscious. Magneto appears and flings Iron Man out of the subway and he lands in a truck.
Tony is still worried about Magneto and his tech. He talks with Pepper and Rhodey until Annie Claremont is introduced. She is taunted by one of the kids in the front row and Pepper as well doesn't like her. Tony and Rhodey however defend her saying she's just shy. The three go to Tony's locker where Annie's backpack is taken by the same kid who annoyed her until she flings him to the floor. She uses her powers to make a bunch of lockers hit him and the kid shouts out that she's a mutant. The hallway goes quiet until Annie runs to the rooftop. Tony and the others follow and tell Annie that she can trust them.
They go out to eat lunch after school where Annie tells the others about her ability to read minds. She reveals she knows Tony and Rhodey are Iron Man and War Machine and needs their help. She tells them about how Magneto is looking for her trying to get her to join his ranks. Suddenly, Magneto Appears!
1st Fight With Magneto
Magneto reveals his iron tracking powers and attacks the group. Tony activates the Mark II but the others are trapped between Magneto and two cars. Annie uses her powers to move the cars and they continue running. Magneto tries to crush them with more cars but Iron Man flies in and punches him. Magneto makes Iron Man fly into various objects and electrocutes him with a traffic light. Annie enraged, uses her telekinesis to make objects fly at Magneto but he turns them around unhurt. Magneto throws Iron Man into a building and his systems shut down. He captures Annie and flies off just before Iron Man's systems come back online.
Magneto traps Annie in his lair where he tells her about Robert Kelly's attempts to segregate mutants.
Tony back at the armory puts on a new Mark II suit and programs the forcefields to counteract whichever magnetic field Magneto is controlling at the time he activates them.
Annie tries to contact Tony and Rhodey but fails because of Magneto's mind stopping tech. Annie throws a bunch of objects at Magneto but doesn't harm him.
2nd Fight With Magneto
Iron Man and War Machine find a building but an explosion goes off. Annie telepathically contacts them and tells them her location.
Robert Kelly speaks about a new law to register mutants and Magneto watches with Annie. Annie refuses to kill Kelly and Magneto tries to kill her. Iron Man and War Machine stop him but he quickly flings Iron Man into a building. War Machine's missiles are controlled by Magneto and he is also flung into numerous buildings. Annie saves Kelly's life which astonishes him. Iron Man then attacks Magneto and his forcefields are able to stop Magneto's control of magnetic fields but Magneto continually attacks Iron Man with objects. Iron Man fires the unibeam but Magneto pins him down. War Machine flies in and takes Magneto's helmet. Annie puts Magneto to sleep and the police take him away. Kelly leaves being booed by fans. The same kid annoys Annie and Tony makes him back off. Annie tells them her name is Jean and Professor X asks her to join his school. Annie smiles and goes with him.
- Iron Man/Tony Stark
- James Rhodes/War Machine
- Pepper Potts
- Jean Grey/Annie Claremont (first appearance)
- Magneto (first appearance)
- Senator Kelly (first appearance)
- Professor X (first appearance)
- Jean Grey and Robert Kelly (voiced by their respective X-Men: Evolution actors) appear in this X-Men-centered episode. Charles Xavier makes a cameo at the end of the episode, though his face remains largely unseen. Jean's alias of Annie Claremont is a reference to acclaimed X-Men scribe Chris Claremont. Also Jean had a friend named Annie Richardson whose death Jean felt telepathically when her powers first manifested. Simon Trask (who is also a human X-Men villain in the comics) is also referenced in the opening sequence of the episode having been attacked by Magneto. Pepper briefly mentions the Weapon X Program. Also, Magneto's real name of Max Eisenhardt is used instead of the usual Erik Lensherr or Magnus, though they are listed as aliases, this for the first time outside of the comics. Finally, Tony again mentions working together with Pym Industries, selling his ideas to the company of Henry Pym.