The MRD starts hunting mutants without warning, forcing the X-Men to strike back. Angel joins the X-Men and tries to destroy the artificial intelligence/multi-agent system, Mastermold, accompanied by the Brotherhood who were betrayed by Magneto. However, the dystopian future still exists and Mastermold had transferred itself to a damaged Sentinel.

After furiously snapping at his father on the development of a so-called "cure" for mutants, Angel's wings are severely damaged at the hands of the MRD and are ordered to be cut off. However, Mr. Sinister then makes him a proposal that will change his life forever, transforming Angel into Archangel and with even stronger angelic wings.

During a battle with Juggernaut, Cyclops is distracted by a vision of Jean and Juggernaut defeats and escapes the X-Men. Emma proposes to erase all memories of Jean from Scott's mind and he accepts. When Emma enters his mind, she looks at all his memories. The truth behind the explosion is revealed to be Jean transforming into the almighty, cosmic Phoenix.