Cyclops and Marvel Girl (Rachel Grey) have been captured by an unknown mutant. Wolverine and Nightcrawler retrieve a tape that Banshee was attempting to bring back to Westchester. He died trying to save a passenger plane from crashing. The tape was a recording made by the late Moira Mactaggert shortly after the formation of the X-Men, and holds dark secrets from the past. Wolverine, Beast and Nightcrawler gather to watch the tape.
In the past, Xavier rushes to see Moira right after he lost contact with the X-Men while they were on a mission, known in the present day as the “Krakoa Incident”. Xavier shows Moira the last moments of the X-Men’s battle with an unknown creature before his telepathic link with Marvel Girl was severed. Xavier is unable to contact the X-Men but Cerebro is certain that they are still alive and stranded. Xavier has come to recruit Moira’s students to carry out a rescue mission.
Back in the present day, Marvel Girl awakens to find her and Cyclops in a strange place. Their captor is nowhere to be found. Marvel Girl’s assessment of the mutant shows that his powers have increased past Omega level and he does not have full control over them. Cyclops recognizes the facility and remembers being here a long time ago. Marvel Girl pulled from their captor᾿s memories of him being in this facility with Cyclops, and was once past of the X-Men. Marvel Girl suspects Xavier of hiding a secret from the X-Men.
Back in the past, Moira reveals the mutants, who were more than just students she was “tryin’ to help”. They were subjects of hers and Xavier’s “genetic research”. Sway had the ability to control time, by slowing or stopping minutes, and see into the “recent past”. Petra could alter the geology of rocks and move the earth. Darwin could change his physical body to adapt to extreme surroundings, including growing gills to breath underwater. And the mysterious Kid Vulcan, an “energy manipulator” whom Xavier showed the most interest in. Not much is known about this orphaned mutant and he refuses to divulge his past.
Xavier approaches Moira’s students for help. Despite knowing the dangers, the prestige of becoming an X-Man is more than enough to persuade the eager students. Xavier brings them back to the Institute and puts them into a mentally-stimulated “crash course” where they will experience months of training in a few hours. Moira has reservations about how Xavier is able to risk the lives of children in battle. He explains to her that mutants live in a prejudiced society, and these children have to be willing to fight for a better future for all mutantkind.
Barely prepared for what they were about to face, Sway, Petra, Darwin and Vulcan are sent to Krakoa to save the X-Men. Right before the mission, Xavier pulls Vulcan aside to discuss in private. Moira had assumed they were talking about the mission details, but there was more to it than that.
Before they can learn more from Moira, the tape breaks down. Beast is not able to salvage more, leaving questions about this secret team unanswered.
Meanwhile, Cyclops and Marvel Girl discover the facility was an old research facility located not too far from the Institute. Xavier helped Moira design this facility, and was where Cyclops met Moira after the X-Men found his brother, Havok. They had run some tests on Havok here, and on a separate occasion, Cyclops visited this facility but cannot remember why.
Vulcan, their captor, reveals the memory that was erased from Cyclops’ mind. Vulcan and Cyclops had met before at this facility, before Krakoa. Vulcan also revealed that he is the long-lost brother of Cyclops and Havok, and that his friends died on Krakoa rescuing the X-Men. And Cyclops had Xavier to thank for erasing any memory of the existence of this secret team.
Vulcan’s past is revealed in his dreams. He was born on another world and grew up as a servant among an alien race. He remembers a kindly old lady who gave him a book on the “Myths of Ancient Rome”, his prized possession and wherein he found his new name.
But on the day his mutant powers manifested, he accidentally killed Dai’Andral, the only one who cared about him. He fled, and somehow ended up on earth in New York city. Then he is discovered by Moira and brought to her facility.
There he meets Xavier and the famous X-Men, “mutant super heroes” whom he and his friends aspired to be. Vulcan’s nightmares started when Xavier helps Vulcan unlocak his memories. Xavier reasons that this is the only way to help Vulcan better understand how to control his powers completely. Vulcan senses an underlying motive, but he doesn’t question it.
Xavier brings Cyclops with him once to meet Vulcan. Vulcan is honoured to have the opportunity to spar with the “leader of the X-Men”, and discovers he is even able to deflect Cyclops’ optic blast. This impresses everyone, and Xavier is considering Vulcan as a candidate for joining the X-Men because of his potential. But only Vulcan knows how deadly his powers can be and keeps this secret to himself.