The Xavier Shelter For Indigent Children:
Sister Nicholas is praying for the children’s welfare. She is accompanied by Sister Debbie, who was scouting the area. They kneel before a painting of the Lord, and pray together. Afterwards, Nicholas tries to explain to the newest Sister what belief is all about.
Suddenly, a noise is heard. They are under attack! Sister Einstein gets thrown through the church’s window. She is dead. Nicholas warns Debra to remember the battle strategies and not to panic. Just then, their attackers move in. Nicholas recognizes them: they are from Atlantis! Debra is ordered to run away, and she does. But she’s too slow, as Debra gets killed.
Elsewhere, X-Nation gets taken away by their captures. Nostromo is in pain, and Clarion fears that he might be dying. They are brought to Avian, who’s furious that Willow is not among them. He taunts December, who doesn’t want to cooperate. That’s fine by Avian, who orders his men to bring the kids to the processing room. In the processing room, Twilight stares at a fellow captive, namely the young mutant Metalsmith. They are both attracted to each other, but don’t say it out loud. Twilight tries to fight back, but with no success.
X-Nation is put into test tubes, and the painful experiments under Avian’s watchful eye begin. As Avian points his attention on the kids in the hope to find the Messiah, he doesn’t notice that one of their guards is replaced by an intruder, who has a familiar looking tattoo on the eye. The “guard” won’t let Avian turn X-Nation into mindless kids. Not now, not ever!
At the same time, Shakti is confronted by Exodus. He wants X-Nation. Shakti of course won’t allow that, so they fight. But Exodus’ psionic backlash is so intense that she loses balance and falls off the roof they were standing on. Exodus rescues her, only to inform her that he wants to rescue the kids from this ghetto they call home, and save them from mankind’s hatred forever.
Shakti senses Exodus’ thoughts, who are nothing but cruel and murderous. Shakti will never join his Acolytes, and won’t let him take the kids. She gives Exodus a neural paralysis with her powers and, while he’s out, she escapes. When Exodus is back to his senses, he notices that Shakti’s gone. Now, he wants her to join him as well. And if Shakti and X-Nation won’t listen to him, they will die.
The battle between the Sisters and the Atlanteans escalates. And the Sisters are losing. They prepare for the worse, but most of them get killed. Nicholas is left. Attuma rises, and shows Nicholas the body of Debra. In a furious move, she attacks Attuma, who grabs her by the throat. He informs his reason of attack: according to their prophecy, the protectors of the false prophet must die.
The experiments have stopped. X-Nation doesn’t want to stay any longer and plan an escape. Two guards show and want to bring them back to Avian. The guard that was taken away attacks his companion, and reveals herself to be Willow! After a short reunion, Willow impersonates Avian in the hope to be able to leave. Despite the tattoo on her eye, the guards think Avian is the real deal and let “him” through. The kids leave in a helicopter.
The real Avian reports to the guards, wanting a plane prepared for his departure. The guards realize their mistake, and Avian orders to get the kids back. X-Nation is already too far away, heading towards home. They invite Metalsmith to stay with them. They are attacked by an Atlantean warship, but don’t recognize it of course. They manage just to dodge the attack but, when they arrive back at the shelter, they are just in time to see it explode!