The game is a simple forward-scrolling rail shooter, similar to the Star Fox series. Only the Game Boy Advance's directional pad, A, and Start buttons are used during gameplay. The ship remains locked at a set speed and cannot brake or speed up.
The player encounters more than fifteen types of enemy, not including level bosses. Some are easy to destroy; others, including the fire creatures found on the Iridion home world, are indestructible and must be avoided. Other enemies prevent the player from dodging enemy fire by laying mines to block paths. Passive objects, such as garbage or asteroids, can damage or destroy the player's craft. Enemies vary in armor and weaponry—some cannot return fire but travel in waves to ram the player.: 19–22 The player's ship can use five types of weapons, with three levels of power each. Players boost weapon power by collecting powerups that match the current weapon's power; collecting a different color gives the player the first level of that weapon type. If the player's ship is destroyed the power level of the weapon is reduced by one. Flashing powerups restore the craft's shields.: 5
Each level has the player follow a linear path through waves of enemies and culminates with a boss. In boss stages the player's craft does not move forward, but hovers in front of the boss. Each boss has a single vulnerability which flashes when hit. These areas are often heavily shielded and must be hit repeatedly to remove armor. Other bosses' vulnerabilities are hidden and appear for only short periods. Most bosses have weapons that fire upon the player or reflect the player's shots. At the end of each level, players receive bonuses for defeated enemies, lives remaining, and the energy level of the player's craft.: 4 An extra life is granted if the score reaches certain thresholds.: 28
In the opening cinematic of Iridion 3D Earth is attacked without warning by the Iridion, who take over much of the surface and lay mines in orbit and bombs in the Pacific Ocean. The player is the pilot of an experimental SHN fighter, the last hope for defending Earth from the Iridion.: 6 The player pilots his ship alone against hordes of Iridion fighters and natural obstacles. The early stages begin on Earth, with the player fighting through an Iridion garbage tunnel. The player proceeds to the Pacific Ocean and destroys much of the Iridion invasion fleet on Earth before heading into the stratosphere to destroy the orbital blockade around Earth and subsequently annihilating the Iridion boss at the Moon.
With the invasion fleet in ruins, the player heads into the far reaches of space. After destroying an Iridion mining colony within an asteroid belt, the player proceeds into the Iridion home system. Eventually the player fights the Iridion on their home world, destroying the Iridion "mainframe" and ending the alien threat forever