Star Trek: Elite Force II is a first-person shooter computer game developed by Ritual Entertainment and published by Activision. It was released on June 20, 2003 for Microsoft Windows and later for Apple Mac OS X. Elite Force II is a sequel to 2000's Star Trek: Voyager – Elite Force. Whereas the original game was powered by the first version of id Software's id Tech 3 engine, Elite Force II is based on a heavily modified version of the Quake III: Team Arena engine with Ritual's ÜberTools GDK, allowing for expansive outdoor environments and higher quality facial animations.

The game begins with Voyager traveling through a Borg transwarp conduit (as seen in the Voyager series finale, "Endgame") when a Borg sphere captures the ship. The Hazard Team, led by Lieutenant Munro, is dispatched to destroy the sphere's dampening field. Voyager then breaks free from the Borg Sphere and returns to the Alpha Quadrant.
A screenshot from the game depicting a shootout between the player and the Romulans in a simulated scenario.

Considered to be redundant, the Hazard team is split up; Munro is assigned to teach small unit tactics at Starfleet Academy. Two years later, Captain Picard witnesses his performance and requests that Munro re-establish the Hazard Team for service on board the USS Enterprise. Shortly after the reinstatement, the Enterprise receives a distress call from the USS Dallas, where Telsia Murphy, a former member of the Hazard Team, has been assigned as a security officer.

Once aboard, the Hazard Team encounters a race of aliens (later dubbed Exomorphs) who have commandeered the ship. After saving the remaining crew, Munro is reunited with Telsia, who joins the team. A nearby Attrexian station which the Dallas had sought to aid is still besieged by the Exomorphs. When the defense systems are reactivated the remaining invaders abandon the station, leaving ion trails which the Enterprise follows to the planet Idryll.

There the Hazard Team locates archaeological post manufacturing the Exomorphs under control of Krindo, his father, and Kleeya (an optional love interest of the main character). The Idryll explain that the creatures turned hostile because of a malfunction. Kleeya later decides to stay on board the Enterprise, which upsets Krindo. His forces invade Enterprise in proximity of another Exomorph-infested colony, Taravar 7.

The Enterprise fends off the attackers and the Hazard team is beamed to Taravar 7, where it aids the inhabitants. In a nearby factory, Krindo's crashed ship is discovered. Munro is captured, but is set free when Krindo witnesses his father's death at the hands of the Exomorphs he created, which no longer obey him. Munro then persuades him to help stop the Exomorphs and the two escape together.

On the Enterprise, Krindo confesses he made money by selling Idryll artifacts to a Ferengi named Omag. He surmises that Omag decoded the location of Master Control Facility, a place with the ability to override all other centers controlling Exomorphs. With Krindo's help, Omag is tracked to a nearby mercenary base and captured.

During his interrogation, Omag reveals that the coordinates to the facility were sold to a secret Romulan group called the Empty Crown. Munro infiltrates the base in a Romulan disguise and with the help of a spy retrieves the location of the Master Control Facility. However, when the informant declares her true allegiance to the Empty Crown, a fight ensues. Gonzalez, one of the Hazard Team members, subsequently sacrifices himself so that Munro can be transported to safety.

The final battle takes place in the Romulan Neutral Zone. Munro enters the facility where the remnants of Empty Crown forces reside under the leadership of Commander Suldok. While the Enterprise is threatened by the Romulan Warbirds for violating the Neutral zone, the final confrontation commences on the surface. In culminates with Munro defeating Suldok and confronting the overmind of Exomorphs, a creature called Archeopendra.

After the battle, Munro returns to the Enterprise, where Picard hands over the evidence regarding the Empty Crown and peacefully leaves the Neutral zone. He is also extremely pleased with the Hazard Team's performance and recommends the incorporation of similar units within Starfleet. In the last scene Alexander Munro is seen kissing either Telsia Murphy or Kleeya, depending on whose invitation he chose during the exploration of the ship.