Legion is a horizontally scrolling shoot-em-up. The player controls a fighter pilot who defends an unnamed futuristic Empire from an assault of mechanical creatures. In spite of the game's exclusively Japanese release, the protagonist delivers voiced monologues in English, musing over his mission, at the beginning of each stage.

The game has a traditional power-up system with a basic weapon power-up that changes its color rapidly when revealed (red for vulcan gun, green for lasers, blue for missiles), as well as assorted collectible letters that either enhance the strength of the gun with additional shots, add a secondary weapon (such as bombs), or provide the ship with a protective shield. In addition, a powerful all-screen attack can be executed by pressing the second action button. At several points during the game the player is able to choose the next stage among two available ones.