The X-Men, comprised of Cyclops, Beast, Marvel Girl, and the Angel, attack the rampaging behemoth known as the Hulk. It is the team’s hope that the Hulk’s alter ego, Dr. Bruce Banner, possesses a device which will allow their mentor, Professor X, to recover from his comatose-like state. In the midst of the battle, the Hulk smashes his fists into the ground, which in turn rips open the underground lab from beneath their feet. Luckily, the Beast is on hand to grab hold of Cyclops and Marvel Girl. Meanwhile, the Angel swoops down and finds the device they have been searching for. With their mission accomplished, the team withdraws in their stolen Sentinel craft, and heads back for their base. The Hulk, content to be left in peace, lets the X-Men leave without further incident.
Later, at the X- Mansion, the team meets up with their remaining teammates, Iceman, Lorna Dane, and Havok. Cyclops activates the small device to their bed-ridden leader unknowing if the device will actually truly help their mentor. As it turns out, the Gamma Rays which are emitted from the device help jump-start the Professor’s mind and he at last awakens. With brief congratulations over their good fortune the full team of X-Men finally is reunited at last.
(Three Days Later / the present:)
Beast, Cyclops, and Marvel Girl are stunned by Iceman’s announcement that he is quitting the team. Despite Jean’s efforts to explain that what Bobby believes about the Professor is wrong, it doesn’t persuade him from changing his mind. Feeling betrayed that the Professor didn’t trust them enough to inform them of his plan to defeat the invading Z’Nox, Bobby doesn’t think he can trust the Professor anymore, much less Jean who had been in on the deception.
Cyclops also tries to convince Iceman that it’s not as bad as it seems, though he may have treated the situation differently, but to no avail. Bobby’s mind is made up, especially after what the Professor did to them in the hangar bay the previous day. Just then, the Professor uses his mental abilities to summon the X-Men to the library, but Iceman ignores the hail and walks off, wishing the X-Men luck as he leaves.
Minutes later, the team, now donning their costumes, enter the school’s library where the Professor is waiting for them. When the Professor asks about Iceman’s absence, Cyclops informs him that he has quit the team. Havok proceeds to ask if he has left because of his relationship with Lorna, but the Professor interjects, stating that Marvel Girl has telepathically given him a full account of Iceman’s departure. With seemingly little concern, the Professor calmly dismisses the act, much to the dismay of Angel who voices his opinion, and is too soundly chastised. The Professor orders the X-Men to open their minds so that he may be debriefed of the team’s actions during the months that he was away.
He learns of their encounter with the Sub-Human known as Grotesk, and his own seeming death at the monster’s hands. He then witnesses the team’s first encounter with Lorna Dane and the hypnotist mutant, Mesmero. To his shock, the Professor is surprised to find that Mesmero was in the employ of Magneto, who claims that Polaris is his daughter.
He witnesses as the team meets up with Cyclops’ long lost brother, and his subsequent capture at the hands of the Living Pharaoh, and the events that followed including the Pharaoh’s transformation into the Living Monolith. From the Monolith, the X-Men were confronted by a new generation of Sentinels who had captured Havok, as well as many other mutants.
The Professor takes mental note of Cyclops’ unique answer in defeating the Sentinels, by convincing them to destroy the primary source of all mutation, the sun itself, which surely would have destroyed them. But he then becomes disappointed that the X-Men put their faith in his former colleague, Karl Lykos. Lykos as it turns out, is a “Non-Mutant Variant”, capable of draining the powers of mutants and transforming into the horror who calls himself Sauron. After a battle with Sauron, the X-Men watched as Lykos committed suicide by hurling himself off a cliff near the Antarctic Circle.
While searching for Lykos’ body, the X-Men found themselves in the Savage Land, where once more they encountered Magneto, and his later demise by his own collapsing citadel.
After their adventure in the Savage Land, the X-Men returned to the States and were confronted by the Japanese Mutant known as Sunfire, whom the Professor takes note to himself to investigate as a possible recruit. The X-Men return to the Mansion only to find the Professor alive and well, and their subsequent encounter with the Z’Nox aliens.
With the mental debriefing at an end, the Professor withdraws his mind. But Lorna didn’t feel at all comfortable with the Professor so casually going through their thoughts. Marvel Girl warns the Professor that he should rest, that he hasn’t complete recovered. The Professor agrees, but he still inquires Cyclops as to Magneto’s final fate, and what steps the X-Men made to ensure that he has in fact died. When he discovers that the X-Men just took Magneto’s death for granted, he becomes furious and immediately dispatches the remaining original team members back to the Savage Land to investigate.
Along the way, the Angel begins to wonder what exactly the Professor was thinking. Not only in chastising them for their actions during his absence, but for treating them as though they were still kids. Cyclops turns to Marvel Girl for answers, but she can’t exactly say for sure. She did, however, sense that something was out of phase within his mind, which makes her wonder if the “cure” they used may not have been as effective as they hoped. The team doesn’t have long to ponder, as the Beast warns them that their approach to the Savage Land is going to be met with some turbulence, at which point the craft begins to veer and spin as if out of control.
Back at the Mansion, Lorna Dane and Havok take a walk across the estate grounds. As they get to know each other better, they manage to come to the conclusion that the Professor wasn’t acting like himself. But not having been actual students under his care, they really didn’t have much to compare with. However, their chat is soon interrupted by Iceman, who tells Lorna that he’s giving her a chance to come to her senses and leave the school with him. When Havok begins to voice his opinion, Iceman shoves him to the ground. Lorna attempts to stop the impending battle, but it’s too late, as Havok begins to emanate plasma energy that pushes Iceman and Lorna back. Iceman transforms to his alternate ice-covered form and throws several dozen ice-spikes at Havok, who promptly blasts them with his own powers. Havok in turn, unleashes a massive energy blast which levels the area around them. Suddenly distraught that he may have killed Bobby, Havok begins to dig through the debris of trees that he has destroyed, only to discover an ice dome which Iceman suddenly bursts forth from.
While doing so, a chunk of ice hits Lorna across the head. Havok berates him for being an idiot, while Iceman attempts to apologize, but Lorna won’t have any of it. She is tired of Iceman’s unwanted advances, from assuming that she was his girlfriend, and never asking what she thought of it or even if she desired his affections. Suddenly, an astral image of Professor X appears before them, and with a powerful, and painful, “yell” gets his students to stop their fighting. But Iceman, now more determined than ever to leave, simply walks away.
In the Savage Land, before anyone can stop him, the Angel jumps free of the ship. It is his hope that he can guide them through the worst of the turbulence. It seems to work, and the X-Men quickly find themselves breaking through the thick cloud layer as they descend into the Savage Land. Seemingly safe now, Cyclops locates an empty patch of ground where they can land. The only problem now, however, is that the turbulence destroyed the ship’s rudder controls. With time quickly running out, and the ship heading towards a large mountain, Cyclops orders Beast to open the dome over the ship. Reluctantly complying, Cyclops proceeds to use his optic beams to blow away the dense vegetation to make way for a make-shift runway.
It all seems to work, as the ship begins to come down for a landing, but all is in vain when one of the landing gears snags and it suddenly began to spin out of control. Crashing off the runway, the Sentinel ship slams headlong into the forest until it finally comes to a stop upside down. The Angel quickly makes his way to the downed ship to help his companions, and finds Cyclops and Beast alive and well.
Marvel Girl though seems to be injured, as the two ground-bound X-Men pull her limp body from the wreckage. Cyclops explains that Jean had protected them with a telekinetic field, but the impact put a terrible strain on her own mind and knocked her unconscious.
Concerned that she may die as a result of her injuries, the X-Men are left with the concern that their only hopes lies in Professor X detecting their trouble and dispatching Havok and Lorna to help them. It all becomes moot, however, when they are suddenly confronted by a tribe of native warriors with spears. Cyclops attempts to make clear that they have come in peace, but the warriors shoot the male X-Men with poison tipped darts. Cyclops and Angel instantly fall prey to the darts, but Beast with his greater stamina, is able to partially resist the drug and counter-attacks his foes. More are were able to fell the Beast however, and the unconscious X-Men are carted away.
After some time passes, Cyclops awakens and finds his companion X-Men, Beast and Angel already awake. They are welcomed by two other members of the Savage Land tribe, who assure them that they were incapacitated until it could be determined if they posed a threat. The Beast argues that that could just as easily been accomplished by asking them, but the tribal leader states that they could have easily lied, and that their way gave them no lasting harm. Just then, Cyclops notices that Marvel Girl is not among them, and when he asks about her condition, he is told that she has already “passed on to the Land of the Dead,” at which point she shows them her empty costume laid out across a table.
Elsewhere, in a much more desolate area of the Savage Land, in a more modernized but dirty city, the Savage Land Mutate known as Amphibious makes his way deeper into one of the citadels. He has come bearing news to his master that the X-Men have returned to the Savage Land. It is then revealed that his “master” is none other than Magneto…or rather, the ghost of Magneto, who vows vengeance against the X-Men who have murdered him.