Ikaruga's gameplay centers primarily around the polarity mechanic. Only bullets of an opposite polarity can kill the player. Same-color bullets are absorbed and converted into energy for the game's special weapon, a homing laser. Switching the ship's polarity also changes the color of the ship's bullets, and shooting an enemy using opposite-polarity bullets will cause double damage. Thus, much of the challenge of Ikaruga comes from careful polarity-switching, choosing between high damage and (relative) invulnerability. This is especially true when fighting bosses, as they often fire bullets of both colors in overlapping patterns. The game also presents navigational challenges where the player must maneuver through continual streams of weapons fire, using their shields to absorb one color while avoiding the others.
Stage 2 boss fight; the player uses the polarity system to absorb the enemy fire.

Skilled players may also perform combination "chains" for points. A chain occurs when three enemies of the same polarity are destroyed consecutively. The more sets of three enemies that are dispatched in a row, the more points are acquired, eventually rewarding the player with an extra chance/life. On the opposite end of the spectrum is the entirely original "bullet eater" or "dot eater" strategy, wherein the player does not shoot enemies, including bosses, which retreat after a set period.