Cyclops decides to put the X-Men together, finally realizing that what is left of mutantkind is protected from its own kind. He assembles a group of teenaged mutants from former students to complete strangers into an small army for and against mutants.
Cyclops starts off with Wolf Cub who is in Paris, paying a visit to Maximus Lobo who has antagonized Wolf Cub several times in the past and is currently powerless thanks to the Decimination. Wolf Cub wishes to kill Maximus but Cyclops, appearing, convinces him not to.
Then he travels to Bakwa, Afghanistan, where Dust is protecting the average Afghani from the Taliban alongside freedom fighters, using her mutant powers to liberate one city at time.
In La Jolla, California, a trash-talking blonde kid named Ink is getting a tattoo in a tattoo parlor illegally and is confronted by the cops. Eric uses his newest tattoo of a biochemical hazard symbol and touches a police officer, making him extremely sick. Eric is arrested anyways. Later, while Ink is in jail, Cyclops, disguised as a janitor, recruits him.
Meanwhile, in New Jersey, Blindfold has a startling prophetic vision in a nightmare that shows her among the new team of X-Men, including an unknown teammate, battling Donald Pierce underground and watches a teammate murdered by Pierce in the final battle. She travels to the ruins of the Xavier Institute to try and interpret her vision as something watches her from afar.
She later goes to a Little Italy type community in Naples, Florida to speak with Rockslide about joining the team and telling him that they will need him, beating Cyclops to the punch. Cyclops reluctantly takes Blindfold back to Westchester along with Rockslide. In the catacombs of the Danger Cave, Cyclops briefs them on their mission, gives them their costumes and shows them their new enemies, the Brotherhood of Mutants consisting of former New Mutants, Magma, Danielle Moonstar, Cannonball and Sunspot.
The teams split up to take on the Brotherhood. Blindfold and Ink take on Danielle Moonstar at her home. While a mysterious force that accompanied Blindfold knocked Moonstar out, Ink betrays his teammate and knocks Blindfold unconscious as well. It is revealed that "Cyclops" was actually Donald Pierce in disguise and he had bribed Ink to betray his team. Ink then delivered the two women to Pierce for his paycheck.
Meanwhile, the remaining team members take on Magma. The Young X-Men struggle and Magma uses her powers to turn Dust's sand form into glass. The team seem near defeat until Wolf Cub risks it and claws Magma with a near-fatal swipe.
Elsewhere "Cyclops" spies on the remaining Brotherhood members--Sunspot and Cannonball. Unbeknownst to him, Graymalkin lurks in the shadows watching him and ready to take him down. Ink returns, not knowing Donald Pierce and Cyclops are one in the same, and lies to his leader that Dani's powers returned and she took Blindfold hostage.
Dust : Could turn into living dust storm
Rockslide : Rock body with super strength and durability. If his body is destroyed, he can form a new body out of rocks around him.
Wolf Cub : Heightened agility, strength reflexes and razor sharp claws and teeth; killed by Donald Pierce
Ink : Non-mutant who receives different abilities based on tattoos of iconic images tattooed on his body
Blindfold : Precognition; reduced to part-time status to appear with the team when her powers are necessary
Anole : Enhanced agility, strength and speed, Camouflage and prehensile tongue
Graymalkin : Invulnerability and enhanced strength when in darkness
Moonstar : Depowered; co-trainer of the Young X-Men
Sunspot : Cells absorb sunlight and can be used for a variety of effects including energy blasts and super human strength; co-trainer of the Young X-Men
Cipher : Mysterious young woman who appeared dressed in a Young X-Men uniform calling Ink to aid his teammates