Season 3 Season three sees several major cast changes. In the beginning of the first season three episode it is revealed that Emma is dead while Adam is also presumed dead (which later turns out to be false). A new fourth New Mutant, Lexa Pierce, joins Mutant X. Mutant X now works for the secret society Dominion, which hires them in most episodes to solve problems revolving around mutants or other genetic problems.
Title Original Airdate # Into the Moonless Night September 29, 2003 301 In the aftermath of disaster, the Mutant X team must deal with the death of one of their teammates, the disappearance of another, the return of Mason Eckhart, and the arrival of a mysterious mutant with an agenda of her own.
Wages of Sin October 06, 2003 302 A new deadly substance falls in the hands of a person who wants to auction it off to terrorists. Mutant X sneaks into the auction and two of their members pose as terrorists.
The Breed October 13, 2003 303 The Mutant X team is brought in to help a military base that has become infected with a deadly disease.
Where Evil Dwells October 20, 2003 304 The Mutant X team must stop a serial killer who leaves clues to his next victims in the form of puzzles.
The Taking of Crows October 27, 2003 305 When Lexa is unknowingly drugged with a lethal substance, the team must race to find the antidote before it's too late.
Shadows of Darkness November 03, 2003 306 The Mutant X team is called in to investigate bizarre activities occurring at a local hospital.
The Hand of God November 10, 2003 307 The Mutant X team embarks on a mission to locate and capture a powerful super-mutant who possesses god-like powers.
Wasteland November 17, 2003 308 Jesse is forced to reconnect with his former fiancée when the Mutant X team learns that her company is involved in the genetic manipulation of crops.
No Exit January 12, 2004 309 A revenge-seeking cybernetic mutant uses his powers to overtake Sanctuary's security system in a plot to destroy Mutant X.
Brother's Keeper January 19, 2004 310 The Mutant X team learns about Lexa's estranged twin brother when he becomes the main target of an underground operation harvesting mutant organs.
Possibilities January 26, 2004 311 Brennan and the Mutant X team join forces with a time traveling mutant to defuse a bomb threatening devastating consequences.
Conspiracy Theory February 02, 2004 312 While Brennan and Shalimar investigate a mysterious plane crash, Lexa contemplates her future with the Mutant X team.
Art of Attraction February 09, 2004 313 As the Mutant X team fights to retrieve a formula hidden in a collection of artwork, Shalimar is given vital information from a mysterious source.
A Normal Life February 16, 2004 314 Mutant X tracks down a rogue scientist while Shalimar breaks away from the team to help Adam save the scientist and uncover the real bad guy.
Divided Loyalties February 23, 2004 315 Brennan is forced to return to his criminal past when Mutant X discovers that his old partner is involved in stealing secrets from the Dominion.
Age Of Innocence April 05, 2004 316 Mutant X unearths an old military experiment involving an age-reversal serum and is surprised to discover that Jesse's grandfather is one of the test subjects.
She's Come Undone April 12, 2004 317 Discovering that their teammate Lexa is the subject of a covert experiment that is controlling her, the Mutant X team hunts for the doctor responsible.
In Between April 19, 2004 318 When Jesse's life hangs in the balance, Brennan must connect to him and lead him through past memories they've shared in order to save his life.
Dream Lover April 26, 2004 319 Mutant X must stop a scientist from cloning women for use as slaves in his ultra-exclusive men's club.
The Prophecy May 03, 2004 320 Brennan battles with a Guardian of the Prophecy to stop the late mutant Ashlocke's plan from beyond the grave of world domination.
Cirque des Merveilles May 10, 2004 321 Lexa's suspicions lead Mutant X to unveil a traveling death camp, which is posed as a circus for mutant refugees and Mutant X's enemy within the Dominion.
The Assault May 17, 2004 322 When the dominion captures Lexa and Jess the team rushes to help. Mutant X find out some information about the creator. Last in series
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