On the first day of their honeymoon, the essences of Scott and Jean were taken from their own bodies and transplanted two millennia into the future.
When Jean awakened, she found herself separated from Scott, and in a strange environment. In the midst of explosions, she manages to free herself from her restraints. Catching a glimpse of her surroundings, she sees many dead bodies. She spots a man, alive but dangling precariously by his arm over the fiery depths below. Jean reaches out with her telepathy and telekinesis, only to discover she has lost her powers. Taking a leap of faith, she throws herself down below, catching the man’s hand in time. Jean instantly recognizes her husband through their touch. Strangely, they retain their psychic rapport.
Making their way out, Scott and Jean find themselves surrounded by armed men and corpses beneath their feet. The leader, Ch’vayre, declares that “the child has been found” and “every one of these traitors [Askani Clan] is expendable.” The corpses are to be “draped about the city forum”. A trooper interrupts him, saying that he bio-scanned two survivors. While Ch’vayre summons his mutant powers to expose the hiding place of Scott and Jean, a soldier self-combusts spontaneously. The attacker is revealed to be Mother Askani (Rachel Summers) who was thought dead “in the first wave”. A weakened Mother Askani takes out the troopers with ease, but is taken down by Ch’vayre with a psionic cocoon. Ch’vayre threatens to kill Mother Askani, and Jean jumps into the fray to rescue her on impulse. Without the aid of her powers, Jean is defeated easily. Scott goes to their aid. Making use of weaponry in substitution for his powers, he stuns Ch’vayre momentarily for the three to escape through a portal into the “bowels of the Askani cloister”, flooded with the blood of those who sacrificed their lives in the recent raid above.
Rachel tells the couple that “two millennia after...the X-Men first defeated him...Apocalypse is triumphant.” He killed all the humans, who were considered to be the weaker caste. A survival of the fittest species. Before Apocalypse, the world existed in “unprecedented racial harmony” in the age of Xavier. Apocalypse shattered that reality. The Askani Clan (“Family of Outsiders”) was established to protect these people. Rachel observed that Apocalyse would take on a new form every few years after burning out the previous host (“spending less and less time in each”) in search for the one that could “accomodate his powers” -- Nathan Christopher Summers. Rachel managed to reach the child first, but he was ill with the techno-organic virus, so the Askani arranged for a healthy clone as a fail safe as only she and a cured Nathan would be able to overthrow Apocalypse once and for all. Her phoenix powers were failing when the entity left her body eighty years ago, leaving only the residue of her once formidable powers. They have to destroy Apocalypse before he has the chance to assume Nathan as his new host.
To accomplish this, the Askani Sisterhood cloned the DNA remains of Scott and Jean’s descendants to create host bodies genetically similar to their originals. With her fading powers, Rachel recreates Jean’s telekinesis and Scott’s optic blasts “which would never have survived the time jump arranged by [her] and the Clan Askani”. Rachel warns them “[her] time is growing near” and it’s up to them to save humanity. She then lapses into a coma shortly.
Scott and Jean, with a comatose Rachel in tow, exit into a strange new world with no one to turn to. Ch’vayre is waiting for them outside with men and weapons. He offers to exchange the child taken from the Clan Askani’s supporters in exchange for Mother Askani. Scott recognizes the infant as his own son, Nathan Christopher Summers. He refuses Jean’s help, wanting her to take Rachel to safety. Jean ignores him; if they were to rescue Nathan, they would do it together.
Jean gives Scott a telekinetic lift onto Ch’vayre’s flying craft. Scott surprises Ch’vayre with his newly recovered optic blasts. Scott claims his son as Jean floods the chamber they’re in to provide an escape route. They drift for twenty miles.
Jean: “It looks as though it’s official...if we’re going to pull this off -- Raise Nathan, overthrow Apocalypse, and liberate all the races enslaved in this era...It’s entirely up to you and me.”
Scott: “To tell you the truth, Mrs Summers, if we accomplish even half of that -- I’d say we had a fairly productive honeymoon.”