- Deathbird (Cal'syee Neramani) (First full appearance)
- Apocalypse (En Sabah Nur)
- Mister Sinister (Nathaniel Essex)
- Sabretooth (Graydon Creed, Sr.)
- Mystique (Raven Darkholme)
- Magneto (Erik Magnus Lehnsherr)
- Lilandra Neramani
- Imperial Guard
- Bishop (Lucas Bishop)
- Captain Britain (Brian Braddock) (Mentioned)
- Magda Lehnsherr (Mentioned)
- Clan Chosen
- Gamesmaster (Jeremy Stevens) (Cameo) (First appearance)
- Karma (Xi'an Coy Manh) (Cameo) (First appearance)
- Mesmero (Vincent) (Cameo) (First appearance)
- Late 1990s
- Axis of Time
- 3999 AD
- Graymalkin Facility (First appearance)
- Cyclops' Visor
- Cable's Computer (Behind the scenes)
- Temporal Transceiver
- Time Portal (Behind the scenes)
- U.S. Tinman (Destroyed)
When Oracle, the psychic member of the Imperial Guard is kidnapped by Apocalypse, Professor Xavier deduces his scheme involves capturing mutants with telepathic abilities. The X-Men are split up to track them down before the villains can, which puts Wolverine and Shard in the middle of a scuffle between Archangel and a ninja named Psylocke.
- Psylocke's brother, whom she claims "fights for the good of all mutants", is the non-mutant Marvel Comics superhero Captain Britain (seen in a cameo in "The Phoenix Saga (4): The Starjammers").
- Shard claims Archangel is "destined to join the X-Men" (though, as Angel, he apparently was part of the team once, as shown in flashbacks from "Proteus (1)", "Sanctuary (1)", and the upcoming "Xavier Remembers").
- Magneto's deceased wife, mentioned here, will play a major part in the episode "Family Ties".
- Wolverine calls Psylocke "black-haired", and Archangel calls her "raven-haired", despite the fact she has PURPLE hair.
- The license plate on Psylocke's jeep reads: THX 1138.