The story of Radiant Silvergun is told non-linearly through animated videos and scripted dialogue between stages.[1] In the year 2520, scientists on Earth have unearthed a giant crystal along with a robot bearing the same serial number as another robot called "Creator" on the Tetra spaceship orbiting around Earth. After the crystal begins summoning enemies to attack Earth, fighter pilots on Tetra board their Silvergun fighters and fly down through the atmosphere to save what they can of the planet. The Silvergun pilots fight through hordes of enemies until they eventually reach the crystal which they destroy. The crystal explodes, engulfing the Earth in a large explosion and killing all humans. 20 years later, the Creator uses DNA from the pilots of the Silverguns to create clones and start humanity anew, bringing the story into a loop.

Radiant Silvergun features a unique and innovative weapons system, with seven weapons available at any time. The player has three buttons to control the weapons; the weapon fired depends on the combination of buttons pressed.