Appearing in "Third Genesis"
- X-Factor (First appearance)
- Mister Fantastic (Reed Richards)
- Emma la Porte (First appearance)
- Unnamed maintenance workers
- Chief Jack Fisher & other naval soldiers
- Unnamed New Yorkers
- Several rent-a-cop guards
- Dean Hauser & Harvard University students
- Irv, Eliot & employees at Harras, Anderson & Brown
- The X-Men (Only in flashback)
- The Avengers (Only in flashback)
Races and Species:
- Humans (Main story and flashback)
- Mutants (Main story and flashback)
- Cosmic Beings (Only in flashback)
- Atlantean-Human Hybrids (Only in flashback)
- Human-Olympian Hybrids (Only in flashback)
- United States (Main story and flashback)
- Scott & Madelyne's home
- New York (Main story and flashback)
- New Mexico
- Worthington's Concorde jet
- X-Factor Plane (First appearance)
Synopsis for "Third Genesis"
Anchorage, Alaska: Scott Summers is outside chopping wood with his optic blasts when he's asked to come inside by his wife Madeyline Pryor so that he can watch their son Nathan while she runs some errands. However, upon entering their family home, Scott is distracted by a television report about the possible Mutant Menace and the government considering the idea of making all mutants register. When Maddie notices this she becomes angry and berates her husband for worrying over mutants and reminds him that he is no longer an X-Man and that he should be focusing more on his family than on the fates of mutant kind. That night when she notices Scott standing outside on the balcony brooding again, Madelyine goes out and apologizes for snapping at him earlier. She expresses her frustrations at the problems their marriage has been having, especially in light of the fact that Scott wasn't there when she gave birth to Nathan. When she asks Scott if their troubles have anything to do with Jean Grey, when he says yes she says no more and grimly returns to bed.
The next day in the New Mexico rockies, Angel, Iceman and Beast are preparing to move on with their lives after the disbanding of the Defenders. With Hank accepting a position at Empire State University and Bobby accepting a job at a new accounting firm it looks like Warren and Candy are going to be left alone, despite Warren's attempts to get his friends to stay and try a new super-hero team, and possibly going back to their roots as X-Men and try to improve human/mutant relations. After saving some construction workers fixing Warren's home, Beast and Iceman pay their leave. No sooner have they left then there is a call on the phone for Warren, on the other end of the line is something that Warren finds almost impossible to believe. With no time to explain things to Candy, Warren flies off on a direct line to New York City.
While in San Diego, a Navy ship pulls ashore and Chief Fisher decides to take one of his young crew members, Rusty Collins out on the town and teach the underage young man what it's like to be a man. While out drinking, Fisher introduces Rusty to a "friend" of his, Emma La Porte, a prostitute who takes Rusty out into the alley for a "good time", when she tries to make out with him, his mutant pyrotechnics powers suddenly kick in and accidentally flare out of control, horribly burning La Porte. Horrified by what he has done, Rusty flees off into the night.
When Angel arrives in New York, he meets with Mr. Fantastic of the Fantastic Four. In his urgency he reveals his wings and almost gets whacked with a can tossed by a mutant hater but is pulled out of the situation by Mr. Fantastic. Taken back to Avengers Mansion,  and taking Angel to the lab below, he warns Warren to take it slow when meeting Jean again after so many years.
Back in San Diego, the military has managed to capture Rusty Collins and contain him. As he is being led into a prisoner truck, Fisher tries to rush the boy. As the guilt ridden Collins is being led into the truck, Fisher tells the boy that Emma was horribly burned and could possibly die and vows to get revenge against him for his actions, cursing him for being a mutant freak.
While back in New York City, in his hotel room at the Waldorf, Warren mulls over the fact that Jean wants to reunite with all her old X-Men allies and considers getting into contact with Scott and telling her about Jean's miraculous return. Finally, he decides that he has no other choice and calls Scott. When Scott answers the phone the news of Jeans survival totally shatters his world and he decides that he has to go to New York. When he tells Madelyne and that it's important that he goes, she tells him that if he leaves to never come back. Scott tells her he has no choice and leaves his crying wife behind.
Days later when Scott arrives in New York, he finds that Warren has hired security at his hotel room to insure that thy have the utmost privacy. When he meets Jean for the first time, Jean is happy to see him and shows a great deal of affection. When Scott attempts to tell her that he is married, he breaks down into tears and tries to get it out when Warren walks in on them, quieting any explanations that Scott could possible give her. Warren and Jean then explain the facts of Jean's resurrection: How when the X-Men were fleeing Stephen Lang's space station, Jean had been replaced by the powerful Phoenix Force which took her form and masqueraded as her, and that it was the Phoenix Force who became Dark Phoenix and in the end sacrificed herself out of love for Scott. Jean goes on to explain how she was placed in stasis on the floor of Jamaica Bay until her body was discovered by the Avengers and revived by Reed Richards of the Fantastic Four. With her explanation done, Scott is shaken more than ever before.
Jean then begins talking about how she has been doing research on the years she's missed and that Xavier's dream of human/mutant coexistence is at a crisis point and with the X-Men working with Magneto she thinks their focus on the state of things is more important then ever. When Scott tells her that he's retired from the X-Men and doesn't provide an explanation his and Warren's apparent apathy over the situation angers her and she uses her telekinesis to smash open a wall and leave. When Warren tells Scott to accompany him in following her, Scott can't bring himself to do it. When Warren catches up with Jean, he admits that she is right however he tells her that he has gotten an idea.
Elsewhere, the Beast is at Empire State University for his interview, only to learn that he has been turned down due to the fact hat he is a mutant. Furious at this racism, Beast strips off his shirt and leaves the building in his own unique way. On his way out he is greeted by Angel who offers him a proposition for a new project. Meanwhile, Bobby Drake slaves over his accounting work when a call comes in from Warren. Changing into Iceman he rushes out of the office eager to return to his adventuring days.
A week later when Bobby and Hank arrive at a new complex that Warren has bought by the New York waterfront they are reunited with Jean. After an explanation of what happened to her, they are told that Scott has gone missing for the past few days and Warren sends Hank and Bobby out to find him. They find Scott out by the docks and learn that he has spent the past few days wandering around and finding all their old haunts as teenagers are no longer there. When Scott tries to explain to them the difficulties he's having dealing with Jean's resurrection and how it might impact his marriage to Madelyne, Beast tells Scott that when he tells Jean she is sure to understand. The two men manage to convince Scott to come back with them and hear out Warren's new idea, telling him that it will be great to have the old gang back together again.
When all together, they meet with Warren's old school friend, advertising and public relations expert Cameron Hodge to explain their new business model: The group would pose as human mutant hunters called X-Factor who would take on clients to hunt down and capture dangerous mutants. However this would work as a secret front for them to train mutants to control their powers. The group would also operate in their mutant identities as a group of mutants known as the X-Terminators whenever their powers are required up front. While the team is a little put off by the fear mongering ad campaign they decide to give the operation a shot.
In San Diego, Rusty Collins has been locked up in a naval prison and to his horror Chief Fisher has been assigned guard duty over the cell block that Rusty is locked up in. When Fisher attempts to shoot Collins in his cell, his powers flare up again, burning the chief's hand and allows Rusty to break out of his cell and escape. Later, when Fisher enters a bar after the ordeal and tells the bartender what happened, the barkeep suggests that he calls X-Factor after seeing their advertisement on TV.
In New York, X-Factor gets the call to go to San Diego, and when Jean goes to get Scott, he is less than sure about the idea but she convinces him to go along with it for her. When they arrive in San Diego, they meet up with Fisher at the bar and they have him lead them to the site where the military has already tracked down Rusty. Slipping away, the original X-Men switch into their X-Terminator guises and use their powers to drive the military off and follow Rusty into a cave. There the boy lashes out at them, thinking that they are going to experiment on him. His surging powers cause a cave-in, but the X-Terminators save him and themselves and Cyclops blasts a hole through the roof of the cave. Upon becoming free, Rusty agrees to go with them and when they change back into their X-Factor guises, they give Fisher his bill for $42,000. Fisher balks at the price until they threaten to "release" Rusty once again, and the Naval Chief accepts the bill, which gives X-Factor a good laugh after they leave. With Rusty agreeing to accompany them back to New York for training to control his powers, Angel finds their first mission a success and tells Jean that X-Factor is going to continue to operate.
Meanwhile, in far off Alaska, Madelyne Pryor sits at home during the early hours of the morning crying as she looks on at a photo of her husband who had just walked out on her. In the background, the television mutely plays an X-Factor advertisement.