Heretic
"First there was Doom. Now comes Heretic!" (Computer Gaming World #126, Jan. 1995)
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Heretic
"First there was Doom. Now comes Heretic!" (Computer Gaming World #126, Jan. 1995)

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Hexen II - Four Horsemen of the Apocalypse
HeXen: Beyond Heretic (Raven Software, id Software / Software Creations, GT Interactive, 1997)
In the 1990s, there were at least 3 separate shared universes for Star Trek games, each with their own unique recurring original characters, ship designs, and species.
MicroProse:
Interplay:
Activision:
Interestingly, Starfleet Command I & II were in the Interplay TOS-era shared universe, while Starfleet Command III was in the Activision TNG-era one.
A couple ship designs from both the Interplay-verse and the Activision-verse have shown up in Star Trek Online, notably the Federation fighters from Starfleet Command and Shattered Universe and the Federation carrier from Star Trek: Invasion.
Also Simon & Schuster produced a bunch of Star Trek games in that same era, but I don't think they had an ongoing storyline or recurring original characters/ships/factions between them like the other publishers did.

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" Forget everything your mother has said about running with sharp objects! " Official Sega Saturn Magazine n19 - May, 1997.
Heretic (1994) Developed by Raven Software
Dark Jedi: "You call using a flak cannon a Jedi martial art?"
Kyle Katarn: "Hey, as long as it works."