The planet Radon is under attack by the Zorgon Battle Star. It's now up to the player in the role as a fleet commander in the Xenon Space Academy to travel to it and defend it from the attack. On the route he will have to overpass many enemies and dangers before having a chance on destroying the Zorgon Battle Star.

Xenon 1 is at its core a fixed screen shoot 'em up. It consists of five levels each with a different take on the genre. The first two levels are similar to Moon Cresta. In the first level the player is up against the Aards, birdlike monsters that move in circles above the player. Sometimes they shoot at the player and sometimes they move down and try crashing into him. The second level works similarly but here the player has to destroy bigger variants of the Aards. These are cloned when hit, with one of the clones diving towards the player and exploding when reaching the base line. The third level is without shooting. Here the player moves through a meteor belt and has to get through it without crashing.

In the fourth level the player arrives at the planet Radon. Here he will be up against paratrons, parachuting creatures that jump towards the player from the top. Depending on skill level there are between 10-30 enemies that have to be shot down. The fifth level is the final battle against the Zorgon Battle Star. To destroy it the player has to hit its moving nuclear reactor. A bonus is awarded depending on how long it takes. On all levels the player has a limited amount of fuel and will die if he runs out of it. To avoid this the player will need to refuel at the mothership's service bay.