Development begun: 1995
Prey went through at least three completely different version in its first three years of development alone. Developer 3D Realms, along with talent from Doom creators Id Software, had a demanding vision that involved multiple alien races, a living space ship and manipulable "portals" (before they were cool!). Unfortunately, this and subsequent visions didn't pan out.
Engineer William Scarboro, who worked on one iteration, even commented in 1999, "In hindsight, portal tricks such as these should be used as tricks, not as an engine paradigm."
Though the game seemed destined to be bogged down indefinitely by technical difficulties, 3D Realms kept at it. Development of the final version began in 2001, when 3D Realms realized they could just license the technologies they needed instead of continually failing at developing them. It was officially announced in 2005 and released in 2006, though whether it was worth the wait is still up for debate.