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 New Mutants or other genetic problems.
|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 New Mutant with an agenda of her own. Brennan is captured and tortured for information. In the end, Mutant X arrives and saves Brennan. They leave, but not before Brennan defeats Eckhart. The last scene is amemorial service for Kane and Emma.
|Wages Of Sin||October 6, 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 theauction 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 mimics
the infamous puzzle killer and leaves clues to his next victims in the form of puzzles. A psionic New Mutant who incarcerated the puzzle killer searches his mind for the identity of the killer, and in the end it is revealed to be none other than herself. She dies attempting to killShalimar.
|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 3, 2003||306|
|The Mutant X team is called in to investigate bizarre
deaths occurring at a local hospital. The children's psychiatric ward burned down years ago and is reopening, but is allegedly haunted by the ghosts of the deceased children. The arsonist was a previous patient who was forced to overcome his fears by facing them while being stressed with an injection of cortisol who still inhabits the hospital. Mutant X finds this patient and tries to help him, but instead of being helped,he commits suicide.
|The Hand Of God||November 10, 2003||307|
|The Mutant X team embarks on a mission to locate and
capture a powerful New Mutant who possesses god-like powers. Mutant X is not the only party interested, their competition knocks down The Double Helix. Shalimar is ejected from the plane and is impaled on a tree. Shalimar is saved by Kristoff, a New Mutant who has the ability to absorb a New Mutant or a Non-New Mutant's wound then heal himself or transfer them through another touch. Then another New Mutant named Terra, a Lupine Feral, shoots Brennan and Shalimar implores Kristoff to save his life. Kristoff absorbs the gunshot wound and appears dead. The traitor within the group no longer has a contact but he is plotting tosell the corpse before Kristoff transfers his death.
|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 thegenetic manipulation of crops.
|No Exit||January 12, 2004||309|
|A revenge-seeking Tele-Cybernetic New Mutant uses his
powers to overtake Sanctuary's security system in a plot to destroyMutant X.
|Brother's Keeper||January 19, 2004||310|
|The Mutant X team learns about Lexa's estranged twin
brother, Leo, when he becomes the main target of an underground operation harvesting New Mutant Organs. Leo's New Mutancy which makes him the universal donor also makes him lose control to his other personalities. Eckhart offers to take care of Leo in exchange Lexa must work for him. He escapes and is avoiding her to protect her from his alternate personality, Troy. Brennan's officiousness gets himself knocked out and as Troy is about to kill him, Lexa is confronted with adifficult choice.
|Possibilities||January 26, 2004||311|
|Brennan and The Mutant X team join forces with a time
traveling New Mutant to defuse a bomb threatening devastatingconsequences.
|Conspiracy Theory||February 2, 2004||312|
|While Brennan and Shalimar investigate a mysterious
plane crash, Lexa contemplates her future with the Mutant X team. A conspiracy theorist, Eddie believes everything revolves around an individual named Kane who has just mysteriously dropped off the radar. He helps uncover Project Contact, the creation of the perfect assassin, but unfortunately is touch killed by one himself. Meanwhile, Lexa decides to sit out this mission, but walks in the last scene just intime to save the day.
|Art Of Attraction||February 9, 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. The formula for a non-polluting fuel is hidden in three paintings. Lexa teams up with Randall Blake, a New Mutant with the ability to transform himself into dark gas and create dark anti-matter shields or blasts with his hands uses his abilities to obtain the last piece. Shalimar and Brennan try to track their mysterious source, who isrevealed to be Kane himself.
|A Normal Life||February 16, 2004||314|
|Mutant X tracks down an ostensibly rogue scientist who
is holding members of the council hostage. Shalimar gets instructions to assist this alleged murderer from Kane to prove his innocence and save the remaining council members. The council does not want the scientistto escape but Kane has a way of making people disappear.
|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. Hayes was killed shortly after planting a key to a disc that contains all of the dominion's research. The Dominion wants Mutant X to locate the buyer as Brennan infiltrates the middlemen. Kane's impeccable timing helps Brennan earn their trust and ironically turns out to be the buyer. Kane's quest for answers leaves him only withmore questions.
|Age Of Innocence||April 5, 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. Kane expresses the need for the research not to fall into the wrong hands, as well as Major WilliamKilmartin. Jesse is left to "make the right choice".
|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 who is responsible. Kane returns and reveals their true enemy as a corrupt faction of The Dominion and calls for war dwarfing theiralteration with Ashlocke or Eckhart.
|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. Shalimar and Lexa search for someone still keptin stasis after the fall of Genomex.
|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. Shalimar receives a call from Feline Feral Gia DuChamps and gets Mutant X involved in this affair. Shalimar and Lexa are cloned and sent in as trojan horses to seduce and destroy the others. The real women are kept sedated andfinally rescued.
|The Prophecy||May 3, 2004||320|
|Brennan battles with The Guardian Of The Prophecy to
stop the late New Mutant Ashlocke's plan from beyond the grave of world domination. A New Mutant created from The DNA of all four New Mutant Classifications is created and Brennan and The Psionic DNA Contributor to find The Child. The Child chooses good and leaves with the woman while Brennan remains with Mutant X. The Precognitive Psionic New Mutantwarns Shalimar of the upcoming battle.
|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 New Mutant Refugees and Mutant X's enemy within The Dominion. Brennan and Shalimar infiltrate and their communication signals disappear off the grid. The leader of the traveling circus is one of Eckhart's sleeper agents brainwashed topurge the world of New Mutants.
|The Assault||May 17, 2004||322|
|When The Dominion captures Lexa, Jesse and the team
rushes to help her, they found out some information about The Creator, the original Kane. Kane detonates The Double Helix to allow Mutant X toescape. Last in series.