Battalion Wars 2 gameplay combines land, sea, and air combat. Unlike the first game, which did not feature naval combat, the sequel has several new sea-faring units: Battleship, Frigate, Submarine, Dreadnought and Naval Transport. Also, the Light and Heavy Recon units from the last game have been replaced by merely the Recon unit which has the Heavy Recon's defense and extra gun and the Light Recon's speed. Including the prologue, there are 20 playable missions, and six factions in the game, including the Western Frontier, Tundran Territories, Solar Empire, Xylvania, and Iron Legion from the last game, and a new nation called the Anglo Isles. The game also allows troops to capture facilities for higher respawn rates, and benefits (such as HeadQuarters, Barracks, Factories, Air Bases, and Docks) that can be used to generate more units.
Battalion Wars 2 also features three separate online multiplayer modes, including skirmish, assault and cooperative. In skirmish, both sides start out with a pre-deployed force with a facilities to replace units that are lost. The main objective of the game is to earn as many points by destroying enemy units. In assault mode, one player is given a siege battalion to destroy the opposing player's assets. The third mode is co-op in which two players join forces to tackle a much larger computer. They are given certain units, forcing them to heavily rely on the other. The lack of multiplayer was among the more commonly cited shortcomings of the first game, but this was addressed in the development of the second, although the game still lacks a splitscreen multiplayer mode.