But some missions give the player a slightly more developed colony to ease the job for accomplishing the missions. The Player's colony always starts out with only the Colony Hub as the command post and a Storage facility to store the processed minerals available, requiring the player to build/upgrade all other available buildings. Each mission has a certain amount of objectives, like mining certain resources, capture, protect or destroy certain buildings, build specific colonies at the Colony Site, which have to be completed in order to complete the mission. The player can choose between the Klingons, Romulans or the Federation to play as, and each race has 14 missions. However, Interplay lost its claim to the Star Trek franchise, and no other gaming company seems interested in the New Worlds storyline However, at the very end of the game's final cinematic, several Metar ships are seen to have survived the detonation of the Shiva device, thus leaving room for a sequel.

At the end of the game, the Tabula Rasa is sealed by the detonation of another Shiva Device, and the planets return to their former dimension. Science scanning of ancient structures on one of the planets eventually awakens a dormant, super-powerful alien race called the Metar, which the three factions must band together against to overcome. The three factions then fight for control of the vast untapped natural resources on these planets.

In the opening cut scene, the Romulan D'talla class Warbird IRW Melak sets off an experimental weapon known as the Shiva Device, which tears a hole in subspace and allows a huge number of new planets to enter (apparently out of nowhere) into an area of space dubbed the Tabula Rasa, which intersects Klingon, Romulan, and Federation territory, as well as the Neutral Zone. Star Trek: New Worlds is set in the Star Trek universe after the events of Star Trek V: The Final Frontier.

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