Voyager travelling through a Borg transwarp conduit (as seen in the Star Trek: Voyager series finale, 'Endgame') when a Borg Sphere captures the ship. There are also limited opportunities for exploring the ship between missions, reminiscent of the 'Virtual Voyager' feature found in Star Trek: Voyager - Elite Force: Expansion Pack. Enterprise-E under the command of Captain Jean-Luc Picard. Eventually, he is transferred to the position of a newly-formed Hazard Team's leader on the U.S.S. During the first few levels, Lieutenant Munro returns to the Alpha Quadrant with the rest of the Voyager's crew and is assigned to a teaching position at Starfleet Academy. In the game, the player reprises the role of Alexander Munro, a Starfleet lieutenant (there is no option to play as a female character in this game, in contrast to the previous game). This section contains spoilers! Content within this section may reveal significant parts of a game(s) story. Hertzler ( Martok from Star Trek: Deep Space Nine, plus roles in Star Trek: Voyager and Star Trek: Enterprise) as Lurok and Vaughn Armstrong ( Admiral Forrest in Star Trek: Enterprise) who contributed several character voices.

Several actors from other Star Trek series provided additional voice acting: Jeffrey Combs ( Weyoun from Star Trek: Deep Space Nine and Commander Shran from Star Trek: Enterprise) as one of the main villains Tony Todd ( Kurn from Star Trek: The Next Generation) as Krindo J. Tim Russ returned to do voice work as Tuvok. However only a few of the primary cast of Star Trek: The Next Generation did voice acting for the game, among them Patrick Stewart as Jean-Luc Picard and Dwight Schultz as Reginald Barclay. Many of the members from the original Hazard Team reappear.

The game's storyline is a semi-sequel to the movie Star Trek: Nemesis, and the end of the Star Trek: Voyager TV series. Unlike the first game, Star Trek: Elite Force II is largely set onboard the U.S.S Enterprise-E stationed in the Alpha Quadrant.

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