As shown at the end of season one, Genomex is defeated while Mason Eckhart is put into a stasis capsule. The main villain is now Gabriel Ashlocke, a powerful New Mutant who however suffers from the fatal side effects of his mutations. Most of the first episodes of season two revolve around Ashlocke and his plans to cure himself from his deadly mutations. After he is killed the next episodes are again stand-alone episodes which follows "The New Mutant Of The Week" pattern.

Title Original Airdate #
Past As Prologue October 5, 2002 201
Ashlocke tries to revive an ancient Egypt alchemist who

possesses the power to cure him, since his mutations will kill him. Mutant X tries to prevent this but they are unsuccessful. The end of the episode has Kane sealing the alchemist's powers with the combination of two triangular amber colored puzzle pieces and an incantation.

Note: This episode deals more as Science Fantasy than Science Fiction.

Power Play/b></td> October 12, 2002</td> 202</td>


Adam sends Brennan and Jesse to prevent an military

official stealing a laser defense system. Nevertheless, the mission fails and Jesse is exposed to nerve gas in his phased state that combines the gas with his DNA destabilizing his Molecular structure. The molecules which ostensibly are bonded to his DNA will diffuse out of his system eventually. The military officer makes a demand holding a nuclear facility hostage in an attempt to lure Mutant X. Kane forbids Jesse to go in his condition. The entire situation was a setup to lure our Jesse and have him physically disengage the fuel for the nuclear core. The rogue military officers leave but are stopped by Mutant X and are vaporized by the very laser defense system they stole.</td> </tr>

<b>Time Squared October 19, 2002 203
The team chases Gabriel Ashlocke to a psychiatric

hospital, where he finds a young New Mutant who has a combination of Molecular and Psionic abilities and he forces her to send him back in time to 1978. Ashlocke tries to heal himself of his own ailment by modifying Kane's original experiments on his younger self. In the Mutant X universe, apparently the ripples in history readjusting to changed events are visible to the characters of this show such as newspaper articles being rewritten and Sanctuary reverting to a mountain. Several more time jumps are shown and they prevent the death of old Kane in the

Whose Woods These Are October 26, 2002 204
Brennan and Shalimar investigate a series of deaths for

which a New Mutant is seemingly responsible. Shortly later they face a cryptozoologist who is accompanied by a group of hunters. The New Mutant is part of Project 318, a space program creating perfect Ferals astronaut. The experiment backfires and they create a virus that infects only Feral New Mutants, and Shalimar gets infected. Kane solves this

problem in the end.
The Future Revealed November 2, 2002 205
Gabriel Ashlocke manages to enter Sanctuary with his

ally Kim thanks to his Telepathic union with Shalimar. His proposal is

to force Adam to heal his ailment.
No Man Left Behind November 9, 2002 206
A military plane is knocked down in an enemy territory,

and the heroes of Mutant X move in to clean up this mess. Their mission is to recover a secret weapon, the PVG, but Brennan's childhood memories haunt him. His father was shot down during the Vietnam War and never returned, making him insist on rescuing the pilot. His foolish heroism leads to his capture. Eventually he escapes and returns with Mutant X, the PVG, and the pilot. Kane is then shown brushing off the threat of a general saying he doesn't always get his way, but times like these make

up for it.
Crossroads Of The Soul November 16, 2002 207
When Brennan gets caught inside an invisible ostensibly

utopian city, which is ruled by a high council that does not want to lose its power, a force field prevents anyone from leaving the city, but some citizens believe there is more than just the city. Brennan is framed for a murder and about to be executed, but the rest of Mutant X

arrive just in time to save him.
Sign From Above November 23, 2002 208
Mutant X realize they are being implacably chased by a

group of aliens who want to capture New Mutants and extract their cerebral spinal fluids as food. Jesse's girlfriend is one of the first few victims. Kane receives intel and sends Mutant X to investigate. Shalimar is captured and later it is revealed that Kane's source turns out to be working with these aliens. Kane finds a way to neutralize the

ingested New Mutant DNA and level the playing field.
Body And Soul November 30, 2002 209
A New Mutant, Cyrus Payton, able to jump from one body

to another uses his abilities to take revenge of Genomex and three scientists who are part of a project called The Walker Project who experimented with him to get a normal life. Emma's Psionic Blast will separate Cyrus from his host, during which he is vulnerable to electric attacks. They use the final surviving scientist as bait and have Cyrus try to control a phased Jesse and fail. Brennan then eliminates the

astral form.
Understudy January 13, 2003 210
When Shalimar gets ill, the team decides to replace her

temporarily. The problems come when her replacement decides that she

wants to remain in Mutant X permanently.
The Grift January 20, 2003 211
A former girlfriend of Brennan comes to Mutant X asking

for help. In addition, she has a surprise: she assures that Brennan is a

father of her son.
At Destiny's End January 27, 2003 212
Emma infiltrates a group of ecoterrorists with being discovered by the chief of the group, who is a Psionic Precognitive.
Within These Walls February 3, 2003 213
Brennan gets injured in a jailbreak during a prison

transfer, which happens to be a New Mutant: Nick Maddox who has the ability to shoot photon daggers from his fingertips. Kane wants answers and the New Mutant wants revenge, and ironically, Kane's contact and the one who imprisoned the New Mutant are one and the same. Kane had a complicated relationship with his contact and they talk things out while trapped in a room. Mutant X functions without Kane and Brennan learns

how difficult Kane's position is.
Hard Time February 10, 2003 214
Jesse and Brennan go undercover to investigate a prison gladiatorial scheme.
Under The Cloak Of War February 17, 2003 215
Adam is the target of an assassination league. After

their first failure, he sends Shalimar to infiltrate the group but the

situation quickly becomes dangerous for her.
Once Around February 24, 2003 216
The team must protect a defense witness against a New Mutant who can project and tune his senses of others that he had touch.
Final Judgement April 7, 2003 217
Adam is put on trial by a mysterious group called The Tribunal for crimes against humanity.
Inferno April 14, 2003 218
The team tracks down a Pyromaniac New Mutant but matters

are complicated when Emma is "possessed" by the spirit of his most

recent victim.
One Step Closer April 21, 2003 219
The team must protect a Senator's daughter but Brennan's powers grew out of control, endangering the mission.
Reality Check April 28, 2003 220
A New Mutant with the ability to manipulate the minds

and perceptions of others sets out to locate Sanctuary, and captures

Shalimar to do so.
Reawakening May 5, 2003 221
The team travel to the arctic to assist one of Kane's

associates' defrosting of The Protocanth, a prehistoric humanoid and unknowingly opening "Pandora's Box". The Protocanth wakes up, hungry, and turns the ship into its own tropical climate. Mutant X eventually contains this creature using liquid nitrogen and they all decide to rebury the creature and leave a warning to postpone the jeopardy

scientific curiosity could cause.
Lest He Become May 12, 2003 222
New Mutants enter the scene and with Jesse's hacking,

linked to Naxcon Corporation Industries, a company owned by none other than Nicholas Fox Shalimar's father. Shalimar's relationship with him is distant at best because of his obsession to be "normal". Shalimar's father, who despises Kane and his genetic research, is shocked to find his new partner, Eckhart, is conducting secretive genetic research right

below his proverbial nose.