Fleet tactics, scientific progress, and defense were primary tactics through this chapter. Throughout that chapter, Starfleet pursued the Borg until finally discovering a transwarp portal leading to the Delta Quadrant, where a daring strike greatly reduced the Borg threat. In Act 1, the player was a Starfleet admiral acting as first-responder to the new Borg threat, with the USS Enterprise-E assigned to that unit. In the single-player mode, players progressed through three chapters which served as a primer to the various tactical scenarios typical to its gameplay. Many important Star Trek dynamics were simulated, such as many types of nebulae, a latinum-based wartime economy, neutral Ferengi traders, and a highly technology-dependent balance of power. Economics, strategy and tactics were equally important.
In Armada II, players acted as admirals in control of an entire theater of operations.
Following upon the storyline of Armada, Armada II centered around a resurgent Borg threat in the Alpha Quadrant in the form of a new weapon, which was capable of conducting wholesale assimilation of a planet from orbit.