Some time ago, at a resort in the South Pacific, two X-Men - Jean Grey and Wolverine - are chained up, with cloaked figures who work for 'The Hand' seemingly casting a spell on the two of them.
Jean reflects that the first time she met Wolverine, she should have "run for the hills and never looked back". She recalls the time she actually tried to leave the X-Men, to find her own way without the X-Men, and attempted in vain to get her boyfriend Scott Summers, the field leader of the X-Men, to come with her. Scott was too invested in Professor Xavier's dream, and so she left, though only for a brief time. Jean recalls how "fate" brought her back to the X-Men, leading her to walking a path that turned "Marvel Girl", into "the Phoenix", which then left her dead for a time, and ultimately revived back to life.
She reflects how every time she looked into Wolverine's eyes, she found feelings in him, which she now feels in return.
Wolverine exclaims that he "can't keep em outta my head!" due to the drugs given to him and Jean. Jean recognizes the combination of science and magic, one to subvert their minds and the other their souls. Jean thinks this must have been what the Hand did to fellow X-Man, Psylocke, months prior when they remade her body and attempted in vain to also transform her soul.
They struggle to refrain from succumbing to the enchantment and believe that there will likely be a physical metamorphosis to accompany the change. Jean worries that Logan won't be able to hold onto his own mind, due to his mortality and having limits to his healing factor, which will no doubt wear him down. Meanwhile Jean's telepathy has been blocked by the villains, preventing her from being able to call for help from the rest of the X-Men. She fears that she and Logan, are the only ones who can save themselves, much to their difficulty.
Jean recalls how they were given the mission by director of S.H.I.E.L.D., Nick Fury, who notes that the X-Men have had a rough time lately, and that they're short handed, but it's a critical situation, and he needs the X-Men's help. Jean thinks that the word "rough" is putting it very lightly, considering the Professor, weeks ago, was able to walk, and is now a paraplegic once again, and the X-Men have no idea why. Fury states that proving how valuable they are might help them change some of the negativity the world feels towards them, and mutants in general. Cyclops notes that they've seen it before, though Fury warns him, that it's worse than what they've experienced before.
Cyclops is quick to dismiss the thought of the X-Men getting involved in S.H.I.E.L.D. business, reminding Fury that the mansion is in ruins, they’ve been through hell, and this time, he'll have to find somebody else to do his dirty work. Jean attempts to speak to him telepathically, only for Scott to verbalize his wish that she would stay out of his head, as he has made his decision, and that he needs to talk to Beast and figure out how they are going to rebuild the Mansion.
Jean apologizes for Scott's attitude that seems to have been building since X-Factor's confrontation with Apocalypse on the moon. Wolverine notes that he thought it had a happy ending, to which Professor X acknowledges the expectations that come from a happy ending, are expectations they feel obliged to fulfill, in Scott's case, not only expectations, but obligations, to his son, and to the mother of his son, Nathan. Logan states that that's life, and that Cyclops should learn to accept it.
Wolverine tells Fury that he'll have to make do with him “an’ the redhead", to which Fury informs them that they would have been his first choice, due to SHIELD’s lack of knowledge of the operation. Logan can use his senses, and Jean her telepathy to "scope out the scene". "Your job is reconnaisance," Fury states to Jean and Logan, advising them to leave the law enforcement to S.H.I.E.L.D., and in the best case scenario, think of it as a nice vacation. Jean thinks to herself, while Logan says aloud "We should be so lucky."
Some time later the pair are working undercover on the island. Jean feels like a slacker, because the rest of the X-Men are busy rebuilding the mansion, while they're having a seemingly wonderful time on a beautiful seashore. Logan states that "someone's gotta do it", before asking if Jean is getting any tender information via her telepathy of some of the patrons of the resort, only for her to respond with a simple "nada". She explains her mind is closed, and she can't sense a thing. Logan thinks somebody around here likes their privacy, to which Jean states that it's more then that, due to all the serveillance cameras all over the place, and all the staff wearing "wires". And with her telepathy blocked off, the two X-Men are cut off from their allies. Wolverine advises her to "have faith", noting that they won't be abandoned. Jean hopes he is right.
Later Jean and Logan are in bathing suits at the beach in the water. Jean asks if Logan doesn't like the water and Logan replies simply, "Nope." Jean comments that he looks pretty good in those trunks. Logan again, replies simply, "Whatever."
Jean reminds him that they're supposed to be newly weds, and they're supposed to be on their honeymoon, so he should try smiling to make their cover seem more realistic. Logan asks if her telepathy is sensing anything yet. Jean replies that she still isn't getting any telepathic signals, and feels trapped inside her own head. She believes that they will have to rely on Logan's senses, and that she doesn't know how to feel after years of wondering what it would be like to have no telepathy.
The day goes on, and after spending the day following employees, Logan hints that he's found something, and that they should go on a "lover's stroll" to check it out after dark. Jean remarks that he's enjoying this. He comments that he can't imagine why.
The pair go for a walk, and Jean holds Logan's hand to Logan's surprise, saying they need to keep up appearances. Wolverine, flustered, states he followed some of the employees to a remote part of the island that has a sign reading "off limits", and is guarded by two resort employees.
They climb up into the mountains of the resort to try to get a better look at the hidden part of the island, as well as possibly getting out of range of whatever is blocking Jean’s telepathy. Jean notes that the view is gorgeous, but notes that her telepathy is still out. Logan wonders why she's so calm considering the loss of her telepathy. Jean informs him, that it's not so bad, and it's good to remember how most people live their lives, never knowing what others are thinking, and being free from the chatter for a little while is refreshing. Logan wonders if she's scared, with not knowing if something is going to happen to them Jean says "not really", besides she has Logan's senses to help watch out for trouble.
Logan warns Jean that sometimes his senses can get manipulated as well, to which Jean asks how? Suddenly Logan pulls Jean in for a passionate kiss. Jean pulls away, clearly shaken and confused, commenting that them being in a relationship was supposed to just be a show. In a near instantaneous appearance, ninjas of the Hand appear, telling the pair of X-Men, that they "coulda fooled us".
Jean and Logan are chained up, with the Hand’s intention clearly being to transform Jean and Logan in a manner similar to what they tried to do to Psylocke. Jean thinks to herself that Logan has been through so much in the past months and he's far weaker than the last time, plus their connection to each other creates a vulnerability that they can't protect against.
She fears that they can't hold on much longer, when Psylocke, Nightcrawler, Shadowcat and Jubilee burst through the wall, coming to rescue their friends. Psylocke charges at the nijas, asking if they remember her, after what they did to her. Nightcrawler warns her to be careful, with Psylocke being shocked at his warning, retorting she's out for blood. Shadowcat looks on, surprised at Betsy's attitude, and finally realizes that the Hand left a psychological mark as well as a physical mark in the form of Psylocke's new body. Kitty goes to help Jean and Logan in order to prevent the same thing happening to them.
Jean warns Kitty to stay clear, that it isn't safe, and not to try to unchain them. Kitty reminds Jean that the words 'unsafe' and 'stay clear' have never meant anything to an X-Man. She tries to phase Logan and Jean free, only for Logan to suddenly attack Kitty and Jean. The transformation has begun, and Logan is now the Hand's personal assassin. Kitty, half unconscious, phases through the ground.
Psylocke and Nightcrawler, fighting the army of The Hand, notice something happened to Kitty, though Nightcrawler notes that they can't do much about that while they're fighting for their lives. Nightcrawler teleports behind one of his attackers to restrain him, while Psylocke continues to fight through the army, one after the other, commenting that she hopes they enjoy her psychic blade, though she wishes it was real. Nightcrawler asks if she would really kill them. Betsy says it's what they deserve.
Jubilee approches Wolverine, ignoring the orders of "the grownups", because Logan is her friend, and she owes him everything. "C'mon old man. Fight your way free of this , just like you did the last time, when you saved me from the Mandarin," Jubilee pleads. Wolverine ignores her and punches her across the face, shortly before unsheathing his claws to prepare to kill his friend. Jubilee begs him not to do it, when Psylocke appears to kick Logan across the face, saying that if he wants to pick on somebody, he should pick on her.
Wolverine mocks Psylocke's belief that she can defeat him, though Psylocke is confident in her martial arts training and can at least hold her own against Logan's adamantium claws. However, Wolverine eventually defeats her, claiming that her powers and skills are nothing, and that he is the "Master Assassin of The Hand", and with his claws he will claim her heart and soul, only for Nightcrawler's tail to wrap around Logan's wrist.
Kurt attempts to restrain his friend, teleporting whenever Logan tries to strike him, however Logan doubts Nightcrawler's ability to stop him, when he refuses to kill him. Nightcrawler gets surprised by Logan and punched in the stomach, winding him. Logan pins Kurt down and is about to strike the finishing blow.
Shadowcat phases down to an underground laboratory, where she sees two mysterious cloaked figures around a generator, chanting, and the generator and chanting seem to be in sync. Kitty feels it's calling to her, and she recalls it feels very similar to when Ogun cast a spell on her to make her his apprentice. She suspects that it may be what is controlling Jean and Logan, so she decides to try and phase through it, in order to disrupt the energy matrix, and maybe that'll set their friends free.
Nightcrawler begs Logan not to do this, that they're his friends, to which Wolverine responds that he is the Master Assassin, and that he has no friends. He intends to kill Kurt, when his claws are telekinetically restrained. Jean reveals herself to be back to full power, and tells him he's wrong on both counts. He is not the "Master Assassin of The Hand", and he does have friends. "One of whom loves you more then her own life!"
Logan states that she's human, and when he cuts her, she'll bleed, "and then you'll scream!" Jean tells him that her heart reaches out to his, what exists between them will not be denied. Jean tells him "It brought me to you, now let it bring your true self back to life, and to me." Logan is freed from his Master Assassin persona, and returned to his friends.
Much later, after the heroes have tied up the mess, and their prisoners have been handed over to S.H.I.E.L.D., Kitty comments to Jean and Logan, that The Hand had things very well covered, since, “asfar as Fury and S.H.I.E.L.D. could tell, You guys were just fine." Logan comments that their friends "knew better" and Jubilee notes that they're not just team-mates, they're family. Nightcrawler adds that they felt something was amiss, and when Kitty couldn't raise them via comlink, nor Betsy via telepathy, they decided to check things out for themselves. Psylocke asks if Jean and Logan care for a lift home? Logan comments saying that they'll make their own way.
As Logan and Jean watch their friends fly home, Logan comments that Jean saved them, and Jean states he would've done the same for her, or any of the other X-Men. Logan states that "it's a whole lot more than that, Jean. You read minds, I read bodies, trust me I know." Jean blushes. Wolverine comments "See. Made ya blush."
Jean asks Logan "if we follow our hearts, how do we know it'll lead to a happy ending?" Logan simply states how he sees it, "Only one sure way to find out. Can you turn your back on the truth, Jean? Will you live the rest of your life as a lie, because you were afraid?" Jean responds with a one word answer.
Jean and Logan come together in a passionate embrace, with Jean acknowledging that "this is my choice."