The game takes place in 2378 and 2380.
The original preview screenshots of the game featured the members of the Hazard Team looking exactly like they did in the original Elite Force game, only with updated Starfleet uniforms. However, after getting feedback from several sources it was decided to fully update the Hazard Team's character models.
Although Star Trek Voyager: Elite Force (2000) offered a choice between playing as either the male Alexander Munro or the female Alexandria Munro, this option did not exist for the sequel. Only Alexander Munro was incorporated into the game.
The Andorian characters in the game are based on the race's redesigned appearance first seen in The Andorian Incident (2001).
This was the first "Star Trek" video game to feature the Denobulans, a species introduced in Star Trek: Enterprise (2001).