The battle at the Tomahawk Motor Lodge has attracted the attention of the police and the National Guard. When an officer attempts to get close enough to investigate, the owner stops him and tells them that the mutant hunters known as X-Factor went inside and his thoughts that they are likely dead.
Inside, X-Factor (in their X-Terminator guises) have revived from their battle against the Alliance of Evil. Cyclops is furious that the group could be betrayed by the Mike Nowlan -- the junkie mutant they came to help -- and be trounced by the Alliance like rank amateurs. His scoldings leads to an argument between him and Marvel Girl, and Jean expresses her frustrations towards Scott's attitude towards her and wonders is it because she isn't the Phoenix or that she lost her telepathy, not hinting at the true reason. When Warren tries to comfort Jean telling him that it's Scott who is the problem and suggests that their leader tell her the truth, Scott lashes out at Warren for getting them together as X-Factor on what he things is a failed endeavor to clandestinely recruit mutants under the guise of mutant hunters. When dodging Cyclops's blast, Angel dives outside of the wrecked motel, and frightens the people outside. With their cover blown, X-Factor makes a quick escape through a hole in the roof. After Warren leaves a bundle of cash behind to pay for the damages, Jean begins focusing on Warren in a more flirtatious manner. Once safely away from the motel, they begin trying to track down Mike Nowlan.
Mike is once more a prisoner of the Alliance of Evil, who are busy terrorizing him and his ex-wife Susan for the trouble caused when Mike escaped from their clutches. They pressure him to reveal who the mutants that they faced were, and Mike lies, telling them that they are a group of mutants that fought off X-Factor. Not completely buying it, they stop focusing on Mike since all he wants is another fix and threaten to hurt Susan until she gives up the information they seek. Enraged by the threats to his ex-wife, Mike's powers flare out of control and as a result boosts their powers to uncontrollable levels. When Stinger's powers flare out of control they blast through the roof of their mansion headquarters, the explosion tipping X-Factor off to their location. When Frenzy threatens to harm Mike if he doesn't shut off his powers, Apocalypse intervenes and tosses her aside, and then forces Mike into a device that nullifies his power and leaves him in a stupor. Apocalypse reminds them that they are gathered together to show the world that mutants are the stronger species before lowing himself and Mike into his underground lab.
When X-Factor arrives at the mansion it is full dark, and Cyclops sends Beast to prowl around the premises and Angel and Marvel Girl to check the roof. Left alone for a moment, Iceman asks Scott when he plans on telling Jean about Madelyne, Scott is more frustrated than ever telling Bobby that being torn between the two women he loves is driving him mad. While above, Angel and Marvel Girl inspect the damage done to the roof of the building. Jean has come to the conclusion that Scott must be in love with Phoenix because of her power and can't settle for ordinary Marvel Girl anymore. Warren tells her that's not it and as he tries to tell her the truth they almost share a kiss when they are ambushed by the Alliance of Evil. Jean just barely has time to put up a forcefield to protect them from one of Stinger's blasts. The sound of battle sends Cyclops and Iceman rushing to their aid, while the Beast locates Mike. Smashing into the lab, the Beast begins trying to figure out how to free him when he is attacked by Apocalypse. No match for Apocalypse's mass altering powers, the Beast is easily knocked out.
While above, Cyclops and Iceman join Angel and Marvel Girl in fighting off the Alliance of Evil. Their battle is interrupted when Apocalypse arrives with Mike, Sue and Beast as his prisoners. Apocalypse has his device remove the drugs from his system and orders him to boost his minions powers or risk the death of his wife. Mike begins to do so, but X-Factor resumes their fight against the Alliance. In the confusion, Sue tries to flee the scene and is struck by a stray bolt fire by Stinger, killing her instantly. Horrified by witnessing his ex-wife being killed, Mike's powers flare out of control, bombarding everyone in the room with power boosting energy. As the battle rages, Cyclops takes a moment to watch Marvel Girl fend off Stinger's bolts, and is almost convinced that the telekinetic energy around her is in the shape of a phoenix.
Beast revives, and as Mike's powers being to flare down, X-Factor manages to fight off the Alliance of Evil. Apocalypse, seeing failure in the midst takes the time to flee the scene, vowing he will return to destroy all of humanity. When the police begin arriving on the scene, the Alliance makes a break for it. As the Alliance escapes, the members of X-Factor are pulled back to Mike, who is now dying, he assures them that while the Alliance guessed there was a connection between X-Factor and the X-Terminators, he never told them the truth. He also goes on to tell them that he wasn't worth the help and that they are doing the right thing trying to help others, then dies. Placing a blanket over Mike's body, X-Factor decides to leave the scene. In the aftermath of everything, Cyclops thinks back to the image of the bird he saw earlier and wonders how it could be possible, more confused than ever he wonders if Jean Grey and Phoenix really are one single being.