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- OverviewSep 29, 2003-May 17, 200422 episodesEpisodes22. The Assault May 17, 2004
- The team uncovers many mysteries surrounding Mutant X after the Dominion captures Lexa and Jesse.
- 21. Cirque des Merveilles May 10, 2004
- Lexa's suspicions lead the team to unveil a traveling death camp posing as a circus.
- 20. The Prophecy May 3, 2004
- Brennan tries to stop the late mutant Ashlocke's plan of world domination.
- 19. Dream Lover Apr 26, 2004
- The team must stop a scientist from cloning women for use as slaves in his club.
- 18. In Between Apr 19, 2004
- Brennan must connect with Jesse and guide him through past experiences in order to save his life.
- 17. She's Come Undone Apr 12, 2004
- A doctor is controlling one teammate by means of a covert experiment.
- 16. Age of Innocence Apr 5, 2004
- Jesse's grandfather is one of the test subjects of an old military experiment.
- 15. Divided Loyalties Feb 23, 2004
- Brennan's old partner is involved in stealing secrets from the Dominion.
- 14. A Normal Life Feb 16, 2004
- The team tracks down a rogue scientist, while Shalimar and Adam try to uncover the real villain.
- 13. Art of Attraction Feb 9, 2004
- The team works to retrieve a code hidden in a series of paintings.
- 12. Conspiracy Theory Feb 2, 2004
- Brennan and Shalimar investigate a plane crash and Lexa contemplates her future with the team.
- 11. Possibilities Jan 26, 2004
- Brennan and the team join forces with a time-traveling mutant in order to disarm a bomb.
- 10. Brother's Keeper Jan 19, 2004
- Lexa's estranged twin brother becomes the target of an underground operation.
- 9. No Exit Jan 12, 2004
- A cybernetic mutant uses his powers in a plot to destroy Mutant X.
- 8. Wasteland Nov 17, 2003
- The team learns that Jesse's company is involved in the genetic manipulation of crops.
- 7. The Hand of God Nov 10, 2003
- The team embarks on a mission to locate and capture a mutant who possesses godlike powers.
- 6. Shadows of Darkness Nov 3, 2003
- The team investigates strange activities occurring at a local hospital.
- 5. The Taking of Crows Oct 27, 2003
- When Lexa is unknowingly drugged with a lethal substance, the team races to find the antidote.
- 4. Where Evil Dwells Oct 20, 2003
- The team must stop a serial killer who leaves clues to his next victims in the form of puzzles.
- 3. The Breed Oct 13, 2003
- When a deadly disease infects a military base, the team helps out.
- 2. Wages of Sin Oct 6, 2003
- The team must stop the auction of a lethal substance that terrorists are vying to acquire.
- 1. Into the Moonless Night Sep 29, 2003
- The surviving members of Mutant X emerge encounter a beautiful, mysterious woman.
