Grid Runner is a futuristic version of "tag." On offense, your objective is to capture the flags around the levels without being tagged or killed. On defense, your main objective is to tag the other player (either the computer or a friend in two-player mode) before he or she collects all the flags.

In each level you will find different colored balls that will help you defeat your enemies. For example, the green balls increase your speed, red increases your magic, and blue increases your agility. The more power-ups you collect, the more efficient you become. You can also use and collect magic points.

Collecting magic points allows you to do one of six things: build a temporary bridge, drop explosives behind you, slow down your opponent, fire a weapon (which can be upgraded or traded), temporarily boost your speed, or teleport out of danger.

The protagonist Axxel and his partner Tara, a pair of freelance space adventurers, are sent on a mission to the Gridonion Asteroid Field, a path between Earth and the Nether-Planets, to find out why ships have been mysteriously disappearing. While investigating a seemingly deserted alien ship in the asteroid field, Axxel is captured by an evil witch, Empress Vorga, who then forces Axxel to play a deadly game competing against her demonic minions. If the player manages to beat all of the 14 monsters, Axxel fights Vorga herself. If he wins, the witch is destroyed and Axxel escapes just before the ship explodes.