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- Season 2 overviewSep 19, 1998-Feb 6, 199913 episodesSeason 2 episodes1. The Little Big Man Syndrome Sep 19, 1998
- Jay pursues extraterrestrial terrorists.
- 2. The Quick Clone Syndrome Sep 26, 1998
- Lazy Jay causes trouble when he makes clones do his work.
- 3. The Heads You Lose Syndrome Oct 3, 1998
- Evil Alpha kidnaps symbiote Troy to claim his powers.
- 4. The Dog Eat Dog Syndrome Oct 10, 1998
- Drekk escapes from a galactic prison and flees to Earth.
- 5. The Big Bad Bug Syndrome Oct 24, 1998
- Edwin, Dung and Moe are out for revenge for the death of Edgar.
- 6. The Jack O'Lantern Syndrome Oct 31, 1998
- A Barthok slave trader is mistaken for an evil spirit and steals one of the Worm Guys.
- 7. The Sonic Boom Syndrome Nov 7, 1998
- Kay and Jay team up with the alien cops to catch Auduzi.
- 8. The Bad Seed Syndrome Nov 14, 1998
- An alien smuggler brings strange seeds to Earth.
- 9. The Fmall, Fmall World Syndrome Nov 21, 1998
- The Fmecks try once again to take over the world.
- 10. The Black Christmas Syndrome Dec 12, 1998
- Santa's elves need help when Santa is kidnapped by Drekk.
- 11. The Supermen in Black Syndrome Jan 16, 1999
- An alien device gives both alien criminals and the agents superpowers.
- 12. The Star System Syndrome Jan 23, 1999
- Alien actors disappear and Kay and Jay are sent to investigate.
- 13. The Blackguard Syndrome Feb 6, 1999
- Elle oversees the startup of MiB's space station; alien mercenaries take over the station.