Summary by CharleyX:
Professor X sits in his study, reading the famous lines of poetry "The woods are lovely, dark and deep, but I have promises to keep, and miles to go before I sleep." Cyclops calls over the intercom to report all clear. Xavier calls for Scott a moment later, and he appears. As he and Xavier talk, Scott's costume changes repeatedly, and Xavier realizes that he's not talking to Cyclops, but to a simulcrum generated from his own memories of his first X-Men. Xavier rises from his chair (astral form not bound by physical injury) and moves to the door. Cyclops gets mad and attacks, but Xavier mentally repels the assault. Suddenly, Professor X is attacked by Magneto's X-Men, skillful recreations of the X-Men during the Master of Magnetism's tenure as headmaster. Charles defeats them easily, though and again moves towards the door, sensing something familiar. It's the Phoenix, who warns him off, then attacks when he advances, blowing Xavier off his feet.

In the real world, Xavier's hoverchair shoots backwards with the force of the psychic blow. Jena Grey catches him, and explains to the confused Professor that they came to Braddock Manor to help Rachel following her battle with Necrom, and that Xavier entered her mind ten hours before. Xavier is shocked, and marvels at the power needed to trap him for so long. Since he Phoenix viewed him as a threat of some sort, Professor X chooses to send Excalibur and Jean into Rachel's mind, gambling that her closer ties with them will keep then safe.

The mutants enter to astral planeand witness the Big Bang. The Phoenix Force is showing them its own memories, from creation to the first encounter with Feron, its first taste of humanity, to its replication of Jean Grey and its fall into the horrors of Dark Phoenix. However, with the strength she gained from the piece of Jean's soul it had replicated and the love she felt for Scott, the Phoenix was able to stop further bloodshed by destroying her human form during the battle with the Imperial Guard on the Moon.

The Phoenix soon returned to Earth intending to return the piece of Jean's life-force it had borrowed. On the way back, though, it sensed Jean's mind floating above New York City, not at the bottom of Jamaica bay where it had left her. Looking more closely, the Phoenix found the astral form of Rachel Summers, future child of Jean and Scott, who had psychically shifted her mind to the past to see why their attempt to change it had failed (the classic "Days of Future Past" story, Uncanny X-Men 141-142).

Through Rachel's memories, the Phoenix lived a lifetime of horrors, from Jean Summers's death in Mastermind's nuclear bombing of Pittsburgh to the fatal attack on the X-Mansion ands the death of her mentor Professor Xavier, to Ahab's brainwashing and Rachel's growing resistance. The Phoenix watched as Rachel finally broke her programming and slammed Ahab into a computer bank, crippling his arms and legs, and as Rachel resisted further mind control and was sent to the internment camp to join the surviving X-Men. Following the raid in which the remaining X-Men died, Rachel threw herself back in time. The Phoenix felt itself a kindred spirit to Rachel, having also lost much to evil, and determined to save Rachel if it could, sending part of its essence to revive Jean and the remainder into the future with Rachel. Arriving in the future, the Phoenix revealed itself to Kate Pryde, who was guarding Rachel's body. Kate was unfazed, but supported the Phoenix's plan to save Rachel, who was the only remaining person she cared about. During the next day's raid on Project Nimrod, Kate activated the Phoenix Force with a post-hypnotic suggestion, and the Phoenix flung Rachel back in time to the 20th Century, where she joined the X-Men and then Excalibur.

The memory trip over, Excalibur returns to the present, and is upset with the Phoenix for tampering with Rachel's memories all this time. Phoenix apologizes - she was only doing as Kate asked. The Phoenix now stands in Rachel's form in front of her teammates, and when they ask, shows them an infant that is the reborn Rachel Summers, who died in her battle with Necrom. The Phoenix is slowly allowing her mind to heal, and will bring her back when the process is complete. The Phoenix leave for the stars, and Excalibur is saddened, feeling almost as if Rachel is dead, and hoping she will return one day.

Epilogue: British bobbies (police) comb a rural town inhabited mostly by elderly people, who have all mysteriously vanished. The cops are stymied at how an entire town could just disappear. Little do they notice strange fairy-like creatures running underfoot, or the flying pig behind them. The also fail to notice the Crazy Gang lurking in an alleyway...