In 2183 humanity discovers an energy source that facilitates travel into new regions of space. Gigantic mother ships collect the newly discovered fuel from the distant energy fields and transport it to Earth. When the fleet is destroyed in an alien attack, the player sets out on a perilous journey home in a small harvester. In Ion Assault, instead of conventional weapons, players use the free energy particles that are abundant in space to fend off swarms of aliens. The particles are bundled and the player is able to shoot them at asteroids and enemy ships. The particles are not destroyed in this process, but are redistributed in space, ready to be magnetically attracted again and re-used. Their random distribution makes for dynamic gameplay and calls for a more strategic approach.

Ion Assault offers four scenarios with gorgeous, detailed visuals, each with different types of opponents, bosses and background themes. In the course of the campaign players get to upgrade their spaceships and will, in turn, be able to affect power-ups that enable things such as an increase in ship speed, or an enlarged collected particles radius. Thanks to special power-ups, such as the ability to create temporary black holes, even large numbers of opponents can be dealt with. Players also get to show off their skills in various multi-player modes, and compare their scores to those of the world's best Ion Assault pilots through online high score lists.