A trapeze performance at the Szardos Traveling Circus in Canada goes horribly wrong when Amanda Sefton nearly plummets to her death, if not for a hasty rescue by the mutant teleportation ability of her foster brother Kurt Wagner, also known as the Nightcrawler. Nightcrawler receives a few broken ribs, and is chastised by his foster mother, Margali Szardos, for changing the cues in the middle of the performance before the net had been rolled out for the performers. Nightcrawler is not as concerned for his health so much as the heartache he feels over Amanda's relationship with the trapeze artist, Werner.
Nightcrawler visits a church, and Amanda Sefton follows him, without his knowledge. Amanda reveals that she cares for him more than a foster brother, and the two share a kiss. They make the decision to leave the circus, to find a new life together. Meanwhile, back at the circus, Margali interrupts Amanda and Werner making out in Margali's trailer, and Margali asks Amanda where her foster brother is. Amanda tells her mother she has no idea, and recommends she visit a local church.
In the nearby woods, Nightcrawler makes a dash for freedom with what he believes to be Amanda Sefton, unaware that his mind is under the control of one of William Stryker's telepathic prisoner, Mutant 12. Stryker's soldiers apprehend Nightcrawler, and transport him to the Weapon X facility in Alkali Lake. Mutant 12's power wears off, and Kurt finds himself in a cell with William Stryker, an inhibitor collar preventing him from teleporting to safety. Stryker interrogates Nightcrawler, but the mutant refuses to cooperate with him.
As Amanda and Margali worry about Kurt's whereabouts, Stryker's soldiers beat Nightcrawler to a bloody pulp for praying. Amanda and Margali are left no other choice but to leave with the circus, hoping he chose to go his own way, as opposed to the alternatives. Back at Alkali Lake, Nightcrawler attempts to comfort Lady Deathstrike in their cell. Kurt believes her dying following her Adamantium bonding process, and she unleashes her claws for the first time. Stryker's soldiers rush into the cell, and Kurt learns that that the Weapon X Project had her claws grafted with the indestructible metal, before they knocked him unconscious.
Amanda and Margali argue over the choices that they've made being responsible for Kurt's sudden disappearance, Stryker gives Nightcrawler the opportunity to kill his abusive guards. Kurt declines such savagery, and reiterates that his love of God will see him through. Amanda and Margali come to terms that Nightcrawler may never return, and Kurt reassures a rapidly healing and unconscious Lady Deathstrike that they will escape from their cell. One of Stryker's guards reveals that Amanda's love for him was merely a telepathic illusion to fool the mutant, and that she could never love a freak like him. The information wounds him more than all of Stryker's physical torture.
Stryker then performs a medical procedure on Kurt to control his mind. He forces Nightcrawler to teleport to the location of the soldier responsible for the revelation about Amanda, where Kurt slashes his throat with a Bowie Knife. Nightcrawler returns to Alkali Lake, where Stryker proclaims it time for the mutant to visit the president. Later, Amanda visits a church in Calgary, and asks God to watch over Kurt, no matter where his travels may take him.