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The Millennium Project was a total conversion mod for Star Trek: Armada that aimed to redefine how the game was played. It added or changed the following:
- New ships and structures
- Additional multi-player maps
- Rebalanced Tech trees
In Star Trek: Armada, players would research special abilities for ships to use. In the Millennium Project, players would research ships instead, and all special abilities were unlocked from the start. It also added a second tier of outpost, the Starbase, added new ships, and also made the Galaxy class buildable. Existing ships, such as the Nebula class, had their models changed to be more representative of the TV show.