"And in a few years, some rebellious little kid is going to turn up at your school with me on his shirt: 'Cyclops Was Right.'"
--Scott Summers to Wolverine
A recent confrontation between the Avengers Unity Division and Scott Summer's revolutionary mutant squad saw casualties on both sides.
Months ago, the scans of the New Charles Xavier School revealed a new female mutant residing in Singapore. The scans showed that the girl was an Omega-level potential. Cyclops was quick to act. He anticipated that the Jean Grey Institute will not be far behind.
Scott's team managed to reach the mutant first. As expected, she was a scared little thing with no idea what was happening to her. Scott calmed her and assured her that she was with her kind. Summers convinced her to come. Everything was fine until Wolverine showed up with the Avengers and a S.H.I.E.L.D. helicarrier.
As Wolverine confronted Scott, Captain America issued a stern warrant: the mutant was to be taken into the Jean Grey Institute. Scott countered that this was a choice reserved for the girl. The girl chose Scott, perhaps terrified at the S.H.I.E.L.D. guns trained at her.
Wolverine should have let them go. Instead, he decided to flex his Avenger muscle. He provoked Scott. Scott did not wish to fight. There were too many civilians. But Wolverine pushed further. Scott had no choice but to push back. Magik tried to teleport them. But Rogue knocked her out. In a matter of minutes, all diplomatic gloves were off. Cyclops did his best to control the tide of the fight to minimize collateral damage. But all it took was a small tactical error. Wolverine sneaked up from behind and drove all his claws into Scott's back.
The battle saw Wolverine and Cyclops once again at each others' throats. The antagonism between the two mutant leaders reached a horrific end when Wolverine dealt Cyclops a mortal wound. On his knees and dying, Scott Summers flashed his "X" salute and unleashed a beacon-like blast into the sky. The lasting image of Wolverine as executioner and Cyclops as martyr shapes the future of mutants and non-mutant superhumans.
The consequences of Wolverine's action are felt in the next few days. Mutant sentiment worldwide saw a condemnation of the Avengers. Riots start to break out as mutants turned against their human tormentors. The image of Cyclops and his beacon blast became the rallying point for a global mutant revolution.
Meanwhile, Captain America speaks before cameras and publicly defends Wolverine's action, calling it a regrettable but necessary solution to the terroristic acts committed by Cyclops against the government. He insists that the Avengers are always ready to serve and protect and make the difficult choices.
The United States supports Steve Rogers and gives him the directive to restore order. He is immediately appointed as an active director of S.H.I.E.L.D. He quickly orders that a sector of the Raft be equipped to contain mutant inmates.
Reed Richards objects to Captain America's militant stance. He breaks ties with the Avengers. Susan later announces that the Fantastic Four will lead diplomatic and philanthropic initiatives to benefit both humankind and mutantkind.
Meanwhile, the Avengers Unity Squad quickly descends into discord. Alex Summers is emotionally devastated by the death of his brother and disillusioned by the brutality of Wolverine’s actions. He leaves the Avengers. Sunfire follows him shortly. Thor confronts Captain America and rebukes him for sanctioning Wolverine's actions. Rogers accuses Thor of hypocisy and reminds him of the cruel nature of war. Thor leaves disgust. He and Rogue later form a new Avengers team away from the influence of Captain America and Tony Stark.
The eruption of mutant violence across the world forces Captain America to field a new Avengers squad specifically equipped to handle possible mutant threats. Anticipating the aggression of Omega-level mutants, Rogers directs Wolverine to lead a squad initially composed of the Scarlet Witch, Wonder Man, a recently returned and reformed Molecule Man, Moondragon, and Red Hulk. Scarlet Witch is horrified at the prospect of turning against her race, especially after her role in the previous depowering of the mutant race. She leaves and later reconciles with Magneto.
Doctor Strange tries to set up a meeting with Magneto and Captain America in an attempt to diffuse the tensions. But it seemed that both men were beyond diplomacy. Doctor Strange leaves and makes his own plans.
In the wake of recent events, tensions begin to flare up in the Jean Grey Institute. The school is targeted by human and mutants alike. Kitty Pryde announces that she is taking over as sole headmistress of the school. She publicly severs ties with Wolverine to protect the school from negative publicity.
Cable becomes distraught at the death of his father. He vows vengeance against Wolverine and the Avengers. He teams up with Psylocke to form a new X-Force. Storm leaves Psylocke's team, frustrated at the recent turn of events. Cable and Psylocke are joined by Domino, Boom-Boom, the original Fantomex, and Deadpool. During their first mission, they recruit the mutant mercenary known as Random.
Emma Frost leaves Magneto and the rest of Scott’s team. She returns to Utopia, eager to rebuild it as a refuge for mutants who wished to remain safe and neutral. Upon the request of Magneto, she brings with her the students of the New Charles Xavier School. She is later joined by Alex Summers, Forge, Sage, Sunfire, and Doctor Nemesis.
When Cable visits Scott's grave, he is surprised to see Nate Grey. Nate Grey tells him that he has come to mourn the father he never had. He tells Cable that he regrets not spending the time to be close to the man who was not only a great leader but also the family he had left. Cable is moved and tells Nate that perhaps there is still time for them to honor their father. From a distance, Cable and Nate are observed by Rachel who has also come to mourn Scott. Before parting ways, Cable leaves Nate with a gift: his Psimitar. He also telekinetically rewires Nate's neural pathways and reconfigures his genetic brand with Askani lore. This effectively restores Nate's powers. Rachel also secretly gifts with him a portion of what little remains of her Phoenix Force echo. This effectively depowers Rachel. She later establishes an underground network of volunteers who transport disenfranchised mutants to areas away from the mutant-human conflict.
Before they all depart, they are jolted by a vision of Scott being reunited with Jean Grey in the White Hot Room.
A few days later, in the Weapon X facility, Magneto begins his preparations. He swears that Scott's death will not be in vain. The Weapon X facility is converted into the headquarters for his new Extinction team. Magneto later raises it into orbit. He is joined by a reprogrammed Danger, and Magik who assumes her Darkchilde aspect. Colossus appears, wielding the power of Cyttorak. He nods at his sister, suggesting that Magik is responsible for the return of his Juggernaut powers. Scarlet Witch also appears, apparently reconciling with her father. The final member of Magneto's team is revealed to be repowered Nate Grey.
Magneto decides to publicly reveal himself and his team on the spot where Cyclops died. He appears wearing his old costume. Before cameras, he issues an ultimatum to the Avengers: Surrender Wolverine or prepare for war. He punctuates his statement by motioning to Nate Grey. Nate envelops the team in a psionic shield and every living organism in a ten-block radius. He telekinetically disintegrates everything within a ten-block radius in a spectacular explosion. Magik then teleports the team back to their orbital headquarters.
Meanwhile, from a sanctuary buried deep beneath the sands of the Gobi, an old despot contemplates Magneto's actions as he watches from dusty monitors. He is surrounded by his four most trusted lieutenants. They proceed with patience, seeking to profit from the chaos as they forward their plan for domination.