"In A.D. 2X00 alien Saya Empire secretly built a "Time space" Frontier Post on the Moon, intentionally intrude the earth... In order to defeat the alien's intrusion, the Earth Defense Arms has launched an unprecedented outer space war with the alien Saya Empire..."

Magincross is a horizontally-scrolling space shooter. The player shoots down waves of alien ships until the boss of each stage is reached. Instead of the usual lives system in most shooters, the player's ship instead has a power bar, which will deplete when the player takes a hit, but can be replenished by collecting power-ups that occasionally appear. After defeating the stage boss, the player moves on to the next stage. There are three stages total.