The issue opens with Jean recapping her decision to make herself and the remaining original X-Men forget their time in the future. "I chose wisely," she says before turning her mind to that fateful day she and the X-Men flew toward Earth on an unfortified space shuttle bombarded by radiation. When it came down to deciding who would pilot the shuttle, she remembers arguing with and incapacitating Scott and pulling rank on Logan, "the irritating new guy," before taking control and eventually emerging from Jamaica Bay as Phoenix.
In the mysterious liminal space Jean currently finds herself, she wonders, "Why had it been so hard to admit I didn't have all the answers? What if I trusted the others and, instead of grabbing control, chose to listen...?" Just then, we see events play out differently as Jean chooses to entertain Logan's slight--"You buckin' for martyr o' the year or somethin'?"--rather than pull rank. "You have a better idea?" she asks. And he does: He suggests using his healing factor to protect him from the radiation as he pilots the shuttle to safety.
Jean agrees to assist him and enters his mind. Scott grabs her and tells her he loves her, which surprises her. "It isn't like Scott to reveal his feelings openly before everyone," she thinks. Just then, Logan interrupts their intimate moment to let her know "the numbers are falling. We're losin' oxygen." Jean guides him in piloting the shuttle, and their psychic rapport deepens. She learns more and more about Logan's past just as the radiation begins to consume him. She decides to increase his healing factor by breaking through his mental barriers, which causes her to learn and experience the full extent of his history and trauma. She is moved to tears and realizes, "By a kind of miracle, he trusted me enough to let me into his mind. He's willing to die. For all of us, but especially for me."
Much like Jean did, Logan pilots the shuttle into Jamaica Bay and emerges from the turbulent waters as Phoenix. Before anyone can question his transformation, Logan declares, "They thought I couldn't hear 'em, that I'd become just an animal, but I understood...every word. I am Phoenix, risen from the ashes of my past...and I will make them pay!" He flies off, and Scott asks Jean, "What just happened?" She responds, "I'm...not sure. I'm locked out of his mind now. All I know is--some power has healed him, changed him. And somehow, he's moved beyond himself. He's going after the people who tried to turn him into a mindless monster. And he's going to destroy them."
Later, Xavier, not once mentioning Logan's heroic act or transformation, suggests "going to Ireland, to Cassidy Keep, where Banshee grew up." Jean attempts to interject, but Xavier doesn't let her. "After what we've all been through, Jean...don't you think we deserve a vacation?" Later, Jean confides in Scott that she doesn't understand Xavier's lack of reaction to Logan sprouting spikes and flying. She tells him she's going to Canada to find Logan, and he offers to go with her. During Jean's aside, she notes, "I've loved Scott since we were kids, wondered at the fire I sensed behind his rigorous self-control. It took all my own restraint not to look into his mind, to reach out and touch the flames."
In Canada, Jean shares with Scott that, although she is "locked out" of Logan's mind, she can "feel him, like a hum, a vibration in my consciousness," alluding to her connection to Phoenix. Scott questions her feelings for Logan, noting, "Even seeing this carnage, you love him. I don't stand a chance." Jean responds, "I...don't. Not exactly. Not the way you mean. But I do know him." Eventually, they find the Weapon X laboratory and Logan attacking and being attacked by several mercenaries. They decide to help him, and he doesn't notice. Scott suggests to Jean that she try entering Logan's mind, but she notes that it's still "shielded" from her. In a berserker rage, Logan lashes out at everyone with spiked projectiles, which Jean shields herself and Scott from. All of the mercenaries are killed.
When Logan realizes Jean and Scott have been with him all along, he states, "They're dead now, all the others. I...could have killed you too." Jean interrupts, "You didn't see us. You didn't know." Logan insists, "Even if I had--you don't understand. I wanted 'em dead. And this fire in me--it made that happen. It became my will. I couldn't stop. I didn't want to stop...Kill it! Kill me...please...while you still can. If you can." Jean tries to reason with him, "Logan! No! Listen! We'll--" But Scott interrupts, stating, "He's right, Jean," before unleashing his optic blasts at full power.
Jean notes, "Its mission fulfilled, its fire rejected, the Phoenix leaves...in search of a different host. Someone passionate. Hungry. Desperate for what it offers." Scott's visor is blasted apart, and Jean calls out to him. "Scott, look at me!" she demands. He responds, "Without my special lenses? Jean, I...can't. You'd die." Jean counters, "I don't think so. You have such discipline. You don't know how strong you really are! Just...try. If anyone can restrain it, control it--" He looks at her and then notes, "I can't...not for long. But it's given me this, to look at you as you are... It's not a being of logic, Jean. It thrives on feeling. On mine...for you. It needs... It loves... It wants... Don't let it use me. Kill me. Do it now!" Jean refuses and kisses him.
Just then, Logan stabs Scott through the head with his claws. "My claws respond to my will," Logan says to Jean. "Like always. An' I'm all claws now. Nothin' but sharp edges. Sharp enough to rip myself apart. Old guy like me...lots 'a baggage...never did stand a chance with you anyway." He shreds himself until he burns to ash.
Once again, in that unidentified liminal space, we see Jean screaming, "No!" Then, she notes, "Wolverine seemed the logical choice. He could survive the radiation. Survive even the impact. But he couldn't survive the Phoenix. Not him. Not even Scott...my distant, passionate Scott. In my reality, I steered the shuttle...I called for help. I let the Phoenix have me. That's not what went wrong. But if not there, then where...?"
"Perhaps..." Jean says as Madelyne Pryor, transformed into Goblin Queen, looms above and beyond her shadow.