In Area 51, a captive Mystique manages to escape when one of the research scientists accidentally lets her guard down while examining her. Using her enhanced shapeshifting skills, Mystique flees the place, seeking revenge.
The Institute is undergoing final repairs and redecorating. All the students are helping out in one way or another with their powers. Jean lifts the satellite dish up to Scott and Logan on the roof. She waves to Scott and catches his eye for quite a while. Scott turns to Logan for advice on matters of the heart.
Scott: “Logan, have you ever, y’know, really cared for someone?”
Scott: “I mean, you felt it so strong that you couldn’t even get the words out.”
Logan: “Yeah once. Most beautiful bike I ever saw. I was so speechless someone else bought it.” (Logan gives the dish a little tweaking, only to find Scott has handed him the wrong tool.) “Not wire strippers, pliers! Use your eyes kid.”
Scott: “The problem is, how’s the guy supposed to know if the girl will feel the same way?”
Logan: “Look, here’s how I see it. I’d like to finish this job before New Year’s. So if you don’t tell her, I will!”
Scott: “Uh, no, that’s okay. I’ll do it.”
In the midst of some sensational thoughts no doubt, Scott is harrassed by a random crow flying into his face.
Meanwhile down by the fountain, Jean is distracted with her own set of problems and almost knocks the fountain's statue into Ororo. Conveniently, Ororo is there to dish out advice as well.
Jean: “Oh, sorry Storm. I’m just, uh, distracted.” (When Jean is done with the fountain, her gaze drifts back to Scott on the rooftop.)
Ororo: “Looks good don’t you think?”
Jean: “Yes. Oh um, very nice.”
Ororo: “You and Scott have grown quite close this year, haven’t you?”
Jean: “Yeah. A lot has happened. Scott’s always been there for me.”
Ororo: “Like the time your powers went crazy. He helped you through that. He was so worried about you.”
Jean: “I owe him my life. And the connection he made with me that day was so strong.”
Ororo: “And something tells me it still is. It’s a good day for new beginnings, and for telling people how you feel.”
Jean: “Hmm, maybe.”
Later that day, Scott and Jean walk right into each other in the hallway of the Institute. While they are on track to admitting to each other their feelings, Kurt happens to teleport in right at that instant with an urgent call from Alex to Scott. Jean gets annoyed as Scott takes his call. Apparently, Alex is stranded in Mexico and wants Scott to go get him. Alex turns out to be Mystique in disguise seeking revenge. She kidnaps Scott and leaves him stranded in the Mexican desert. In the evening, Scott’s optic blasts attract the wolf pack.
Back at the Institute, Jean awakens from a nightmare in the library. She had a vision that Scott was being attacked by wolves in a desert. Professor Xavier hears Jean’s screams and wheels into the library.
Xavier: “Are you alright, Jean?”
Jean: “Professor, Scott’s in trouble.”
Xavier: “Or could it be that you just had a nightmare?”
Jean: “No. No something’s wrong. I sensed it.”
Xavier: “Jean, Scott is too far out of sight, of range, even for me. Jean, don’t worry. A bad dream is usually that. A dream.”
At that time, Scott is struggling to fight off the wolves. His blasts attract a couple of nearby oil riggers. Scott falls off the steep face of a cliff, and is rescued by the workers. Mystique is peeved that her plan was foiled and morphs into a bird to follow the workers’ jeep.
Unnerved by her nightmare, Jean gives Alex a call. She learns that Alex never met up with Scott that afternoon, and that her vision was more real than it seemed.
Scott is brought to a hospital for medical treatment by the workers. Scott refuses to allow the doctor to proceed with an examination for a concussion for fear that he might hurt them with blasts. Pinned down, the doctor manages to force open Scott’s eyelids, and the blasts put a hole in the roof. Scott seizes the chance to flee from the hospital.
Fortunately for him, Professor Xavier was able to track his general location to Mexico City with Cerebro using that trigger of his optic blast. Xavier says he isn’t able to “pin point” Scott’s exact location, Jean is determined that she’ll “find him”.
Scott wanders the streets of Mexico City blindly while Xavier, Jean, Storm and Wolverine set out to find him. Scott walks into a group of thugs. He frightens two off with his blasts, and the third thug reveals herself to be Mystique. During their scuffle, Jean catches a glimpse of Scott’s vision through their mindlink and heads for his direction.
Mystique chases Scott into a warehouse. During the fight, Scott gets his leg stuck in the wooden floor, and brings Mystique down with him into the basement by blasting the ground beneath her feet. Scott destroys the lights as well, to use the darkness to his advantage. The cunning Mystique uses Scott’s emotions to her advantage and disguises herself as Jean. Scott finds it suspicious that Jean was able to track him “right to this warehouse” and attacks Mystique. An angered Jean finds Mystique and telekinetically attacks her.
Mystique: “How sweet, girlfriend to the rescue.”
Jean: “You got that right, lady!”
Defeating Mystique, Jean lowers herself to Scott’s side and holds him in her arms, cradling his head to her chest.
Scott: “Ugh, Jean?” (Scott collapses in Jean’s arms.) “Is it really...ugh...”
Jean: “It’s me.” (Jean caresses Scott’s face reassuringly.) “Don’t worry, Mystique is gone.”
Scott: “I can’t believe you even knew where I was.”
Jean: “It must be a bond we have. I don’t know how to explain it.”
Scott: “You don’t have to. I just wish I could open my eyes and see your face.”
After Scott is brought back to the X-Jet, Jean hands him his glasses for the third time in the series and helps him put them on.
Jean: “Okay, go ahead. There, is that better?”
Scott: “It couldn’t get any better.”
Scott takes Jean’s hand. Jean leans in and gives Scott a peck on the cheek, and then rests her head on his bare shoulder. The three adults look on, smiling.
Logan: “Well, it’s about time.”
Ororo: “That’s for sure.”
They turn to look at a smirking Charles Xavier, who is piloting.