The game takes place in 2378 and 2380.
This was the first "Star Trek" video game to feature the Denobulans, a species introduced in Star Trek: Enterprise (2001).
This marks the third time that Andy Milder has played a Bolian. He previously played Boq'ta in Empok Nor (1997) and Brex in Star Trek: Bridge Commander (2002).
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.