When Lexa and Jesse are captured by Dominion forces, who want to know about Jesse's altered genetic structure, Adam, Brennan and Shalimar do their best to rescue the pair. Along the way, they learn many of the mysteries that surround mutants and the Dominion; and meet the mythical “Creator.”
Brennan and the others face off against the Guardian of the Prophecy (Timothy Burd), who is involved with the Links, a nefarious group that is plotting to take over the world. Riley: Monika Schnarre. John Bishop: Wayne Best.
Shalimar receives a frantic phone call from an old friend (Jennifer Steede), leading the team to investigate a gentlemen's club that uses female clones to entertain its clientele. Sebastian: Ted Whittall. Nolan: Matt Gordon.
A figure from Jesse's past shoots him with a bullet that will detonate if anyone tries to remove it and blackmails the X team into locating a mutant for him. Brennan, meanwhile, mind-links with Jesse in an attempt to keep his friend from passing out and dying. Dr. Robinson: Ellen Dubin. Dr. Harrison: Andrew Gillies.
The team discovers that Lexa has been the subject of a covert experiment named “Project Nine” that controls subjects using brain implants. Adam returns to try and help remove the object from her, and the team hones in on the scientist behind the plot. Dr. Gonsalves: Peter Crockett. Dr. Arnot: John Blackwood.
When the team investigates an old military experiment that involves an age-reversal serum, Jesse learns his grandfather (Desmond Scott) is one of the test subjects. Dr. Denise Saunders: Heidi Van Palleske. Dr. Francis Gallant: Patrick Garrow.
Brennan goes undercover after his former partner (Daniel Petronijevic) steals a key to a safe-deposit box that holds a computer disc containing the Dominion's genetic research. Brennan is thrown for a loop, however, by Adam, who reveals himself to him. Nick: Aleks Paunovic. Ethan: Robert Seeliger.
Adam appears in holographic form to a surprised Shalimar, asking her to work with a scientist (Shaun Smyth) to free Dominion Council members who've been kidnapped and frozen by a villain. The Council, meanwhile, suspects the scientist of being the mastermind behind the plot and orders Lexa to capture him, pitting the X team against Shalimar. Anthony Gervais: Sten Eirik.
The team works to recover a code hidden inside three pieces of artwork that will threaten world security if it falls into the wrong hands. Meanwhile, Shalimar receives information from a mysterious source. Blake: Lyriq Bent.
The team link a plane crash to a secret military project that was involved in genetic research. Lexa, meanwhile, contemplates her future with Mutant X. Eddie: Jason Schombing. Silver: Jack Duffy. Benedict: Matt Cooke. Dr. Robert Harrow: Graham Harley. Senator Richards: Philip Craig.
Lexa learns that her estranged twin brother (Steve Byers), who's also a mutant, has been targeted by a nefarious underground ring that harvests mutant organs. Carter: Tome Barnett. Candace: Jennifer Vey. Bain: Alex Karzis.
The team's investigation into genetically mutated locusts leads Jesse to reconnect with his former fiance (Krista Bridges), who runs a major agricultural conglomerate that would benefit if locusts ate all of the vegetation in the world---save for a pest-resistant corn created by the conglomerate. Nate: Sasha Roiz. Dr. Bellows: Shannon Lawson.
Lexa reveals her employer to the others. Meanwhile, the team is dispatched to locate and capture a super-mutant who has the power to heal people. Kristoff: Peter Stebbings. Terra: Jeanette Roxborough. Cody: Shane Daly. Burke: James Bulliard. Carl: John Ralston. Wayne: Johnny Goltz.
The team hunts a serial killer who leaves clues to his next murder at the crime scene and who seems to have a telepathic connection with an imprisoned murderer. Lexa: Karen Cliche. Andrea: Pragna Desai. Lee Marker: Joe Scoren.
The team hunts for a lethal substance that a nefarious casino owner (Deborah Odell) is planning to auction to any of a number of known terrorists. Lexa, meanwhile, pursues the case on her own when she learns of a connection to the mysterious Dominique (Jennifer Dale).
The aftermath of the plant explosion finds one team member dead and Adam missing. A mutant named Lexa (Karen Cliche) joins the search for Adam, but not all of the other members want her help; and Eckhart (Tom McCamus), who survived the blast, offers a swap: the return of Adam for a cure to his genetic disorder. Brennan: Victor Webster. Shalimar: Victoria Pratt.