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- Season 5 overviewSep 7, 1996-Sep 20, 199714 episodesSeason 5 episodes1. The Phalanx Covenant Sep 7, 1996
- The X-Men rush to investigate a disturbance.
- 2. The Phalanx Covenant Sep 7, 1996
- The X-Men are attacked by a race of aliens seeking to assimilate all life on Earth.
- 3. Deal With the Devil Sep 14, 1996
- Omega Red is thawed and sent beneath the ocean to recover a nuclear submarine that threatens Hawaii.
- 4. No Mutant Is an Island Sep 21, 1996
- Cyclops leaves the X-Men and goes back to the orphanage where he grew up.
- 5. Longshot Oct 5, 1996
- Longshot, a rebel from another world, tumbles into this world with no memory.
- 6. Bloodlines Oct 26, 1996
- Nightcrawler gets a mysterious message that the birth mother who abandoned him is in trouble.
- 7. Storm Front Nov 2, 1996
- Arkon begs Storm to help him save his planet from meteorological chaos.
- 8. Storm Front Nov 9, 1996
- Preparations for a wedding proceed quickly; the X-Men discover that Arkon is a tyrant.
- 9. Jubilee's Fairy Tale Theatre Nov 16, 1996
- While trapped in a cave with some schoolchildren, Jubilee weaves a fantastical fairy tale.
- 10. The Fifth Horseman Feb 8, 1997
- Fabian Cortez kidnaps Jubilee to serve as a host body for Apocalypse.
- 11. Old Soldiers Feb 22, 1997
- Wolverine recalls a mission he underwent alongside Captain America.
- 12. Descent Sep 6, 1997
- The origin of Mister Sinister begins with Professor X's father and Nathaniel Essex.
- 13. Hidden Agendas Sep 13, 1997
- Sam Guthrie's parents contact professor Xavier about their son's mutant powers.
- 14. Graduation Day Sep 20, 1997
- On the verge of Magneto's final stand against humans, the X-Men ask him to save a dying professor X.