The X-Men have returned to the grave of the late Professor Xavier to pay their respects, each member lost in thought over what the Professor meant to them and what the future of the X-Men will be. Their vigil is interrupted by FBI agent Duncan, who has come to speak with the X-Men. Returning to the Professor's mansion, Nelson & Murdock co-partner Foggy Nelson is on site to read Xavier's will. To everyone's surprise, all of the Professor's assets have been willed over to Scott for the operation of a special charitable fund, also naming the other students as trustees, leaving behind all his possessions to them. After the will reading is completed, Foggy leaves to put the will through probate, allowing for the X-Men to return their attention to Agent Duncan who wishes to discuss an important matter with them.
While in the distant Crimson Cosmos, the Juggernaut is pulled out of the other dimensional realm he has been trapped in since his last encounter with the X-Men by one of the Professor's machines. Re-materializing in the lower levels of the mansion, the Juggernaut begins to trash the place. Hearing the ruckus, Scott excuses everyone from Agent Duncan and they change into their X-Men uniforms and go investigate. Finding the Juggernaut causing the commotion, the X-Men confront him and learn that the Juggernaut once more wants to get revenge against his step-brother Charles Xavier. The X-Men explain to the Juggernaut that Xavier is dead, to which the Juggernaut rages in disbelief, believing that it's a trick to fool him and he attacks the X-Men.
The Juggernaut manages to shrug off the X-Men's attack and continues his rampage through the mansion. Finding Agent Duncan, he demands to know where Xavier is. When Duncan also states that the Professor is dead, the Juggernaut knocks him out and continues his fruitless search. The X-Men revive and follow after him and find the Juggernaut at the Professor's grave raging that he has been cheated out of his revenge.
The X-Men continue their fight with the Juggernaut, this time with Jean using her newly acquired mental powers against the Juggernaut causing him pain. The Juggernaut grabs the downed Angel to use as a hostage to make Marvel Girl cease her attack. When she does, the Juggernaut is surprisingly shunted back to the Crimson Cosmos. Cyclops deduces that while the machine that was responsible for bringing the Juggernaut back to Earth worked, its effects were only temporary. Surmising that the Professor wanted to be certain of the Juggernaut's rehabilitation, he must have put in a fail-safe just in case the Juggernaut had not reformed.
With the battle over, the X-Men are once more confronted by Agent Duncan who tells the group that the government, realizing that the X-Men would prove to be too easy a target to evil mutants has demanded that the X-Men split up and spread out across the country immediately.
Returning to Xavier's Mansion to ponder this, Cyclops, as deputy leader, decides that despite the unconstitutional nature of the FBI's request, that it is in their best interest to follow the request. With a heavy heart, he orders the X-Men to disband and follow the government’s orders. Shortly thereafter, the X-Men pack up their things and part company, leaving Scott at the mansion. Each of the X-Men is left wondering where their future will take them.