Season 2

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>
		October 12, 2002
		202
	
	
		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.
	
	
		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 
		past.
	
	
		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.