As the Starfleet Lieutenant Alexander Munro returns to Alpha Quadrant from a long voyage, the authorities consider the Hazard Team that he had commanded an unnecessary luxury, disbanding it and assigning Munro to teach small unit tactics at the Starfleet Academy. Two years later, Captain Picard contacts Munro and offers him to reassemble the Hazard Team on board his space ship, the USS Enterprise. Shortly afterwards, the ship receives a distress call from USS Dallas. Apparently, members of a mysterious alien race known as the Exomorphs have attacked the ship. As Munro is sent to rescue the crew members, he is reunited with an old friend, and has to face dangers graver than anything he has encountered so far...
Star Trek: Elite Force II is a sequel to Star Trek: Voyager - Elite Force. It is set in the Star Trek universe, chronologically overlapping with the last episodes of the Star Trek: Voyager series. Like its predecessor, it is a first-person shooter in which the player controls Alexander Munro (who can only be male in this sequel), who is usually aided by his AI-controlled teammates during exploration of the levels and combat.
Munro has fifteen weapons at his disposal, most of which have been ported from the previous game. Most of these futuristic, Star Trek-themed weapons are energy guns that have alternate firing mode. The tricorder reappears with a new function: the player must now actively use it in order to bypass security, participating in a power-routing mini-game, during which it is necessary to connect two nodes by manipulating a series of pipes.
During certain scripted events, the player can choose between two or more responses to a particular situation. These choices may affect the subsequent events and the level progression. There is also a possibility of a romantic involvement with one of the two female teammates.