Summary by CharleyX:
Phoenix III is in attack mode telling the X-Men she's gone to kill the Beyonder. Rogue stands in the doorway to Rachel's room and watches the holographic message play, then zooms up to Storm's attic and explains what she saw. Storm summons the X-Men, blaming herself for not anticipating this. Rogue figures Ray's been gone for hours, and Logan and Kitty think the Beyonder's had it coming for a while. Storm feels they must stop Rachel, if only to keep her from angering the cosmically-powered entity.

Soon, Magneto uses the Cerebro unit in his office to locate Rachel, a process made more difficult due to the magnetic interference he created years ago. Logan is quick to point out that fact, and the two men grate on each other. Magneto picks up Rachel heading towards San Francisco, but the readings are off the chart, and the X-Men wonder in horror if Rachel might be Phoenix in fact, not just in name?

Elsewhere, the Beyonder contemplates his purpose as he studies a flower from the atoms up. He wants to make people feel good and realize their own true purposes. He also contrasts the finite nature of the flower (and all of Earth's creatures) with his own infinitude, but wonders if he simply has not found the proper means to his own end. As if on cue, Phoenix reaches the Bay area, and spots the Beyonder on Alcatraz. She lands and detonates her power in a mushroom cloud of cosmic fire. To her dismay, the Beyonder still stands, and proclaims his intent to do no harm. Phoenix fires again, but with no effect. The Beyonder tells her it is futile to keep trying, and that all he wants is unity, unlike the fractured mortals among whom he walks. Rachel quips about him taking the easy solution to life's troubles, and the Beyonder indeed turns into an avatar of Death.

Suddenly Rachel is back in the ruined New York of her past, as Death-Beyonder forces her to confront her guilt over those friends and family whom she survived. The Beyonder shows her images from that era: the death of her lover Franklin during the X-Men's escape from the prison camp, the deaths of all the X-Men in the Baxter Building, and Kate Pryde's last stand against the super-Sentinel Nimrod, after she sent Rachel to the past.

Rachel is doubled over in grief, and the Beyonder understands why she fights so hard to protect her loved ones and prevent such tragedies from ever occuring again. However, he says, this guilt and fear prevents Phoenix from evolving. He offers Phoenix the power to kill him, and won't even defend himself, though his reasons are his own. He grants Rachel the power and she becomes a being of pure energy and wonders if this is how her mother felt upon becoming Phoenix. Now the Beyonder offers a choice: kill him or save the X-Men.

Rachel sees the Blackbird suddenly appear in the air and knows the Beyonder set this up. Storm is inside, and Rachel contacts her. Phoenix also senses the rest of the X-Men scattered around the city. Suddenly an Omega-class Sentinel rises out of the Bay, shocking Rachel, since they weren't designed until after the turn of the 21st century! She blasts the robot, but holds back on her full power as she is unsure how to handle it. Rachel hears from the others X-Men that more Sentinels have appeared at their locations, and Storm tells her to assist the others while she deals with the Sentinel Rachel downed. Ray quickly leaves the Beyonder to help her friends.

Meanwhile, Storm gets the recovered Sentinel to follow the airplane as she tells Rachel to maintain a psi-link between her and the rest of the team. Then Storm turns the Blackbird vertical and beins to climb into orbit as the Sentinels grabs a hold of the plane. Storm braves the g-forces and structural stress to get above the atmosphere, where she quickly retros and flips over, dislodging the Sentinel, already burned from the exhaust, which burns up on re-entry. Unfortunately, the Blackbird isn't in much better shape, and it begins an uncontrolled re-entry as well.

In downtown SF, Magneto faces off against a Sentinel, which quickly wraps him in a non-metal catchweb. Rogue comes up from behind, but the robot senses and blasts her away. Her costume in shreds, Rogue lands in the crowd that has gathered and absorbs some of their psyches. The rest of the crowd are about to beat her up when Wolverine appears and warns them off, then takes a slice out of the back of the Sentinel's head. However, the unit still functions and it backhands Logan into a wall. The robot fires to disintegrate him, but Rachel blocks the beam and puts up a shield around Logan while she super-charges his power and gets him and Magneto out of the way. She has Logan free Magneto, who stresses that they must get the civilians away. Rachel does this with a telepathic message, and then sets off a bright flash that provides enough distraction for Logan to take out the Sentinel's legs.

The battle isn't over as the Sentinel's self-repair systems go to work, but Magneto isn't yet strong enough to neutralize gravity or otherwise directly affect the non-ferrous robot. Instead he creates a magnetic reverse vortex that brings down cold air from the upper atmosphere, encasing the Sentinel in ice and bringing a rare snowfall to San Fran. Rachel uses her powers to make Rogue's mind dominant again, though she can't remove the psyches she absorbed. She then has Rogue bash through the Sentinel, shattering it. Meanwhile, Magneto uses the vortex to safely lower the Blackbird to the ground.

Elsewhere, Colossus is having a tough time with another Sentinel. The robot knocks him down and stomps on the armored Russian. Fortunately, Shadowcat phases Peter into thre ground, saving him. Colossus reappears shortly, grabs a streetlight and swings it at the Sentinel. Amazingly, it passes right through the robot's body. Then Colossus lets go, and the Sentinel short-circuits as the pole solidifies. Kitty phases herself out of Peter's body, which masked her from the robot's sensors and allowed him to pull this stunt. Rachel arrives, grabs a live power cable and touches the pole sticking out of the Sentinel, blowing it away in a blast of energy.

Shortly thereafter, Rachel returns to Alcatraz to see the Beyonder. He hopes she's made her peace with herself, but she's fuming at him for setting up such a dangerous situation. She slaps him across the face and leaves, telling him that with his approach, he can only do harm.