The Watcher tells of an alternate reality where the new X-Men never existed.
When the original team of X-Men (consisting of Cyclops, Marvel Girl, Angel, Iceman, Havok and Magnetrix) set off to investigate Krakoa, instead of being ambushed and captured by the living island, the X-Men are able to overpower and defeat Krakoa. This victory led to Xavier never forming a second team of X-Men to rescue the original team.
The X-Men return safely, and continue with their routine superhero duties. When Xavier begun to experience “nightmares of an interstellar conflict”, he decides to take some time off. As the X-Men see him off at the airport, they are attacked by Eric the Red, assisted by Nightcrawler and Proudstar (two mutants who would have otherwise joined the second team of X-Men). Eric the Red was sent to assassinate Xavier. The X-Men swiftly defeat Eric the Red and Proudstar, but Nightcrawler escapes.
Xavier decides it is time to tell the X-Men about the top secret facility on Muir Isle, headed by Moira MacTaggert. This facility is designed to contain dangerous mutants, and they are taking Eric the Red there. On Muir Isle, the X-Men are suddenly contacted by former team mate Beast. The Sentinels have resurfaced and captured Xavier and Marvel Girl, who had remained at the mansion. The X-Men journey into space to save Xavier and Marvel Girl, but are left stranded in a damaged shuttle. When Marvel Girl volunteers to sacrifice herself, and an anxious Cyclops trying to talk her out of it, Magnetrix breaks up the argument and offers a win-win solution. Marvel Girl would have encountered the Phoenix Force while piloting the shuttle through the “solar storm”, if not for Magnetrix’s ability to use her powers of magnetism to guide the shuttle home from the safety of the “shielded life-cells”.
Dr Corbeau: “We need someone who can do both [pilot the shuttle and survive the flare], and there’s no such animal.”
Marvel Girl: “Wrong, Dr Corbeau...”
Magnetrix: “I can--”
Marvel Girl: “...I can do both!” Cyclops: “Are you crazy, Jean--? Since when are you a qualified astronaut?” Marvel Girl: “I’m a telepath, Scott, remember? I can absorb all Dr Corbeau knows about flying the shuttle. I won’t be great but it’ll be good enough to get us down.”
Magnetrix: “I can--” Cyclops: “And how will you survive the solar flare?” Marvel Girl: “My telekinetic powers will screen out the harmful radiation--I will be alright.”
Cyclops: “For how long--?! Even your power--”
Magnetrix: “Will you two shut up?! I can bring this shuttle down to earth without the computer--without piloting skill--without even leaving the shielded life-cells! I have magnetic powers, remember? Sheesh!”
Marvel Girl: “...Oh.”
With that, the X-Men return home safely again. They are pleasantly greeted by the return of Beast to the X-Men as well. They learn that Eric the Red had been turned over to S.H.I.E.L.D. and Xavier has a talk with the government about using “public funds” to put mutants’ lives at risk. Life returns to normal for the X-Men, until they are visited by Lilandra. Lilandra seeks the help of Xavier and the X-Men to stop her brother D’Ken from destroying the universe. It was also D’Ken who previously sent Eric the Red to assassinate Xavier.
The X-Men are teleported to the “M’Kraan Plane”. With the assistance of the Starjammers, they defeat D’Ken’s imperial guards and the guardian of the M’Kraan Crystal. They then encounter a sphere trapping the Crystal’s “anti-power”. Cyclops gets the team to amplify his optic blasts to break the sphere and restore balance to the universe.
They return home, and their adventures soon take them to Japan where they fight alongside and befriend Alpha Flight. Seeing Wolverine, leader of Alpha Flight, and Mariko spending time together gives Scott the courage to propose to Jean. Although Jean accepts, she also pulls away in a strange behaviour. Jean confides in Scott about her “time slips” and encounters with a strange man. Upon further examination, Xavier diagnoses Jean as having been psychically attacked. But duty calls for the X-Men and tracking down Jean’s attacker will have to wait.
A chance encounter at the Hellfire Club leads Jean to identify her attacker, Jason Wyngarde. Before the X-Mean can face off with the Hellfire Club, they are teleported to Lilandra’s ship. There is a galactic crisis involving the “Chaos-Bringer” which is about to destroy the sun. Lilandra sends for Xavier and allows the X-Men 24 hours to come up with an alternate solution to relocating the entirety of Earth’s population when the sun is consumed.
Cyclops’ solution is to allow the Chaos-Bringer to possess a human host instead and sacrificing himself to kill the force. Cyclops volunteers himself. But just as he prepares for his final mission, he is knocked unconscious by Nightcrawler, who had stowed away and overheard of Cyclops’ plans. Seeking redemption for his sins, Nightcrawler makes the ultimate sacrifice in Cyclops’ place.