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.
|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 thepast.
|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 thisproblem 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 isto 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 makeup 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 Xarrive 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 theingested 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 theastral 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 shewants 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 afather 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 learnshow 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 thesituation 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 mostrecent 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 capturesShalimar 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 jeopardyscientific 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 rightbelow his proverbial nose.