San Diego, California: As the members of X-Factor sneak onto the air-field where they parked their plane. They seek cover so they are not spotted in their X-Terminator's uniforms. They overhear a television broadcast where reporters interview Tower following his capture after their battle. Tower tells the press that there is some connection between X-Factor and the X-Terminators because both groups have appeared almost practically together every time he encountered them. The Beast causes a distraction for the personnel on hand so that they can board their jet unseen. When pressuring Jean to open the hatch of the plane, Scott in his frustration with her accidentally calls her "Maddie". When Jean asks Scott who Maddie is he angrily boards the ship. Aboard the plane, Jean considers this new person after she thought Phoenix was her rival for Scott's love, and Scott broods over how he thought he saw the Phoenix form shape around Jean during their battle against the Alliance of Evil and how this complicates things even more. Iceman turns on the television and begins watching the media frenzy trying to make a connection between X-Factor and the X-Terminators.
When X-Factor returns to New York, they have changed back into their X-Factor uniforms to greet the throng of press, and protesters that have gathered around the X-Factor Compound. They arrive just as Beast's girlfriend Vera is talking to inquisitive reporter Trish Tilby, Hank manages to pull her away before she can say anything that can incriminate X-Factor and pull her back into their headquarters. As they enter, Cameron Hodge goes outside to address the media, his tone and choice of vocabulary to describe the X-Terminators as "mutant murderers" make the group once more wonder if what they are doing is truly helping mutants. When Rusty and Artie offer lunch to the returning heroes, Scott snaps and tells them that he has to make a phone call. As Scott resolves to finally bite the bullet and tell Jean about Madelyne, Jean wonders what could cause such a behavior from the man she loved.
Meanwhile, in a New Jersey garbage dump, two mutants named Glow Worm and Bulk are scavenging for a refrigerator coil for the well learned Glow Worm to use. Bulk instead finds a mouse that the slow witted mutant wishes to keep as a pet. They are soon chased off the property by guards with guns who try to shoot them. As Glow Worm holds them off with an energy blast, they retreat into the sewers. There, Bulk notes that his new pet has just died, Glow Worm points out that the radiation that the two emit from their body is a threat to any living things around them and is threatening to kill them as well. Bulk wonders why they must hide and after seeing a flier for X-Factor, Glow Worm is inspired that they must do something inspiring to get back at the humans that hunt and persecute them in some profound way.
As the protests outside the X-Factor compound continues, Scott tries to track down where Madelyne may have went and comes up with no leads. While down in the training room, Jean suggests that she, Bobby, Hank and Warren play a game of tag. This is actually just an exercise to distract her teammates into accidentally revealing what big secret Scott is trying to keep. Although none of her comrades out right says it, Jean manages to deduce that Scott is married to some woman named Maddie and storms out of the room in tears.
While down below, Glow Worm and Bulk pass by Skids, a new Morlock who's force field powers prevent Masque from disfiguring her face. She warns them that they are not welcome among the Morlocks as they are dangerous. Glow Worm has only come to tell the Morlocks to stay away while they commit their final heroic acts for mutant kind: destroying X-Factor.
Back in the compound, Rusty confronts Beast and Iceman and tells them that the government is still looking to arrest him for injuring a woman and wonders if it would be any good to talk to the press outside and tell them why he is here, however Hank and Bobby don't think it's such a hot idea. Just then Artie bursts in and shows them an image of Glow Worm and Bulk. Realizing that these two mutants mean trouble, the rush to find Scott and see him looking out the window with Warren as Glow Worm and Bulk attack the crowd outside. With the press outside they cannot appear both in their mutant costumes and operate as X-Factor without arousing suspicions if there are not enough X-Factor members present. With Jean not answering her pager, Scott, Hank, and Bobby decide to go out in their mutant guises while the others try and come up with a means to encounter Bulk and Glow Worm as X-Factor.
Finding Jean in the training room, Warren manages to convince her to forget about her issues for now and help out because Scott could be in trouble. Outside, Cyclops, Beast, and Iceman come up from the sewers to "aid" Glow Worm and Bulk in escaping, chanting the term "X-Terminate X-Factor!", causing Trish Tilby to angle the story dubbing the two "mutant terrorists" as the "X-Terminators". They pretend to "help" Glow Worm and Bulk, when in reality their "bungling" trips up the two mutants until they learn their plot: Glow Worm reveals that the two of them had been contaminated by toxic waste and they intended on infecting X-Factor with radiation poisoning. Seeing them as a threat to everyone, Cyclops orders Iceman and Beast to try and co-ordinate a means to get the dangerous mutants away. Just then, Warren, Jean, Vera, Cameron and Rusty come out of the complex in X-Factor uniforms to give off the appearance that X-Factor is getting involved in the battle.
With Jean and Rusty manipulating their powers to make it look like they are using high-tech weapons, Cyclops manages to convince Glow Worm and Bulk to retreat with them back into the sewers. There they try to convince Bulk and Glow Worm that they can go some place where they can learn to control their powers and live a normal life. However Glow Worm points out that they are so hideous that they could never pass for normal humans, and that not even the Morlock's will accept them thanks to the fact that their bodies are contaminated. With no other choice, Cyclops, Iceman, and Beast realize they have nothing that they can practically offer them. Thanking them for nothing, Glow Worm and Bulk head into the sewers to continue their bleak and measured lives. Upon returning to the surface, Cyclops commends the ground for their teamwork in helping convince the press and the public that X-Factor and the X-Terminators are two separate groups. Jean isn't so happy about the situation and tells Scott that they are in need of a serious talk.