A Son's Revenge
David Haller ( Legion), son of Charles Xavier ( Professor X) and Israeli diplomat Gabrielle Haller, had spent many years of his schizophrenic life in a coma following a battle between the Shadow King (who had possessed David) and the X-Men. Suddenly, in a response to the presence of Mystique, David awakes, his fractured mind healed into one single personality with one single goal -- to help his father achieve his goals of peaceful coexistence between humans and mutants. David targets Erik Lehnsherr ( Magneto) as the true adversary to Xavier achieving his dream. His solution is to travel back in time approximately 20 years and murder Magneto before he adopts his anti-human policies and becomes Professor X's enemy.
Battle For The Past
A team of X-Men, consisting of Jean Grey, Storm, Iceman, Bishop, and Psylocke, arrive in Israel in order to stop Legion, who has destroyed everything the Israeli army has thrown at him. In the ensuing battle, Storm realizes Legion's plan, but only after Bishop is knocked unconscious attempting to absorb some of Legion's powers. Storm orders Psylocke to mind-link to Bishop, who still possesses some of Legion's chronal energy, causing the X-Men (with the exception of Jean Grey, who had telekinetically anchored herself) to teleport along with Legion. Before she passes out, though, Jean is able to contact Professor X and the rest of the X-Men in order to alert them to Legion's plan.
Back In Time
The four X-Men and Legion arrive safely in the past, though the time travel erases all five of the mutants' memories. Legion arrives at the hospital at which both Xavier and Magneto, both young and friends, work. Following a touch from Magneto, Legion experiences a psychic backlash that causes him to project visions of Magneto's past. Magneto gets angry and storms out and Legion apologizes, but this energy starts to awaken Legion's memory. In the present, Jean Grey, Professor X, and Cable pool their energies and send Cable back in time to alert the four time-stranded X-Men, who had got jobs working at the docks. Cable appears to them and, although they don't recognize him, Bishop thinks he looks familiar and touches him, causing the temporal energy surrounding Cable to reach the others, awakening their memories as well.
Battle For The Future
Legion, disguised as his father, Xavier, appears to Gabrielle Haller at the hospital. He seduces her. At the docks, Xavier gets a psychic warning, alerting him that something is wrong with Gabrielle. With Magneto in tow, he runs to the hospital to find Gabrielle disheveled, on the floor, clothes torn. Suddenly, Legion appears behind the two men and threatens Magneto. The X-Men, memories restored, quickly rush to the scene of the fight, only to find Magneto and Legion locked in battle high above in the sky. Bishop and Iceman work on controlling the damage, while Storm and Psylocke attempts to find Xavier. Iceman, who finds himself much more powerful tries to defeat Legion, but to no avail. Legion grabs the defeated Magneto and starts to deliver his murderous blow, but at the last moment, Xavier throws himself in the way of the blast, getting killed instantly, but saving the life of his friend in the process. With Xavier's death, Legion and the X-Men disappear. Only Bishop remained, due to the fact that he was a time traveler and, therefore, a chronal anomaly in the first place. Magneto, defeated but alive, is left to cradle the lifeless body of his friend, Charles Xavier.
With Xavier out of the picture, the Age of Apocalypse is ushered in and dominates the X-books for four months.
Though it is not a part of the official canon of Legion Quest, X-Factor #108 is an important read because it chronicles when Legion actually wakes from his coma. Then proceed to the Prelude before reading X-Factor #109. After that, there is a vignette in X-Men #39 of Legion wandering the Israeli desert and receiving instructions from Destiny. The story then picks up with the first numbered issue of Legion Quest in Uncanny X-Men #320.
An anomaly with this arc is that seven issues are included but only four are numbered as such. It's possible that this is because the events of the non-numbered issues happen concurrently. Or, that Marvel only numbered the X-Men titles for some reason.