As this issue's title implies, Rachel has gone looking for the Beyonder so that she can destroy him and put an end o his rampage once and for all; she believes the Beyonder represents a cosmic threat that only the might of the Phoenix can annihilate. Rogue discovers the holographic message that Rachel left behind, and rushes to warn the other X-Men about Rachel's plans. The team argues about her plan, some even wish that Rachel succeeds as the Beyonder is a threat to the entire planet. In Magneto's office the X-Men use Cerebro, their mutant-detecting device, to locate their revenge-driven friend and find her in San Francisco, amazed by the power levels she now wields according to Cerebro.
On Alcatraz, the Beyonder ponders on the meaning of life and discovers that in order to live well you need a goal in life, hence the Beyonder needs a goal : he will become a healer and a teacher. Suddenly, Rachel assaults him with all the power and fury of the Phoenix and destroys Alcatraz with what looks like a Phoenix-shaped H bomb - to no avail : the Beyonder stil lives and he even protected the island and ist surroundings. He tells Rachel that he only has good intentions, but the X-woman doesn't believe him and vaporizes him good. No dice : the Beyonder still stands and tells Rachel the universe will die before he does; he tried to understand the meaning of life and always was disappointed by those who answered him. All what the Beyonder seeks is unity. Rachel still wants to kill him, and the Beyonder says that this is always her solution, as she has known nothing but death. The Beyonder then transforms into Death and Rachel finds herself witnessing the events of her dark future timeline again. One by one the X-Men were exterminated by the Sentinels. He also shows her Kate Pryde getting killed by the ultimate Sentinel Nimrod after she sent Rachel to safety into the past.
Rachel breaks down, and reality is back to what it was. The Beyonder understands Rachel is ashamed of her past and terrified of her future. He offers her the chance to kill him by giving her enough of his power to rwally harm him, but won't give her his reasons. Rachel is endowed with the power of one thousand galaxies and is given a choice : rid the universe of the Beyonder ... or save the X-Men, who are being ambushed by a series of Sentinels in San Francisco.
The first target is Storm whom the Beyonder transported in the Blackbird over Alcatraz. She is being attacked by an Omega-Class Sentinel, the same kind that destroyed Rachel's world, and shouldn’t exist in this time. Rachel knows she could vaporize the Beyonder in one second but she is needed elsewhere. So blasts the Sentinel attacking the Blackbird and telepathically communicates with Storm. Rachel senses that the other X-Men are attacked in San Francisco, and Storm says that she and the Blackbird can deal with this one Sentinel, so Rachel departs. Storm makes the robot follow the jet and then starts to fly up into the sky faster and faster. Still the robot catches up and grabs the Blackbird, but as the jet flies out of earth’s atmosphere, the robot’s systems fail. Storm steers the jet back to earth, but the plane too was majorly damaged by the stunt.
In San Francisco, Magneto, Rogue and Wolverine face a Sentinel, but Rogue gets blasted and is thrown into a crowd. With her costume torn, she accidentally absorbs their many thoughts and gets lost between the many voices in her head. Meanwhile Magneto got entangled in a non-metallic catch-web and Logan gets slammed into a wall, rendering him unconscious.Rachel arrives just in time and enhances Wolverine's healing factor to save his life, then protecting them all in a telekinetic shield, she tells Wolverine to free Magneto with his claws. Eventually, Rachel, Magneto and Wolverine manage to destroy the robot, but a magnetic vortex of Magneto triggers a snowstorm in the middle of the city. Rachel ponders on how all this power could help people instead of causing so much destruction, she then tends to Rogue and helps her to focus on her own voice among the many absorbed psyches.
Elsewhere, another Sentinel attacks Colossus and Shadowcat, identifying the latter as "Ariel", Kitty's codename in Rachel's future. The Sentinel knocks Colossus down and attempts to kill him by stomping on the X-Man, but Kitty is faster and phases with him into the ground. Rachel arrives and crashes into the robot, making him fall. Inside Colossus, Kitty phases them both back to the surface, and they grab a streetlight, that they phase through the robot. They are happy that the new trick worked and watch as Rachel connects an electric cable with the streetlight, frying the robot’s inner circuits.
After the battle, Rachel returns to Alcatraz and listen to what the Beyonder has to say for himself, pissed off that the X-Men will put weeks to help repairing San Francisco. The Beyonder tells Rachel that she saved the X-Men from Omega-Class Sentinels, thus relieving herself from her guilt. Rachel smacks him one : she did accomplish nothing, the entire situation was arranged by the Beyonder, she was used by the Beyonder like a puppet. The Beyonder says that he wanted to help her restore her inner balance, as he is searching for his own. Rachel tells him that knowledge and maturity must be won and deserved; agrily she leaves.