Star Trek: Armada II is a real-time strategy game set six months after the events shown in the original game. The Borg have managed to survive the cataclysmic Omega particle explosion and are once again invading planets deep in the Alpha Quadrant. Meanwhile, a powerful rogue Cardassian force lurks to seek vengeance on other races. There are now only three singleplayer campaigns - Federation, Klingon, and Borg.
There are two new playable races in addition to the original four: the Cardassians and Species 8472. There are new resources: metal (gathered through planets) and latinum (gathered in latinum nebulae, useless to the Borg); Species 8472 harvests any resources to "bio-matter". Arsenals of all races have been vastly expanded with new ship types, stations, and special weapons. Trading stations allow for trading between players, as well as a secondary source of latinum via Ferengi cargo ships. Planets can now be colonized in order to accelerate the influx of new crew members, and ships' vital systems can now be upgraded in the late game. The 3D world can now make use of the height axis, so ships can move in and stations can be constructed in different height levels. Skirmish/multiplayer maps can now be generated randomly.
USS Incursion, the special operations ship with the holographic disguise system, from Star Trek: Away Team, makes a guest appearance in the final mission as a ship that can move among the enemy ships without raising suspicions.
