The premise of Herzog Zwei is that two opposing forces are in combat with one another. Each player controls a jet airplane which zooms across the screen and may turn into a ground-based soldier. These ground soldiers can hurt enemy units, but cannot affect bases. To take over bases scattered across the map (and ultimately, the enemy base), players must purchase new units and transport them to certain positions. In this way, the player acts more like a transport and management for different types of units rather than a combat character themselves. If the plane is ever destroyed, it restarts at the player's base location. As previously mentioned, a level is complete when either side's base is lost to the opposing forces.
Gameplay involves navigating the battlefield, managing resources, and using ground soldiers to take out enemy units. Players must strategically deploy their units and manage their resources effectively to gain an advantage over their opponent. The game requires a combination of tactical thinking and quick reflexes as players navigate the fast-paced action.