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Wireless Mission is a multiplayer mode in Metroid Prime Pinball. It is done through Nintendo DS Download Play, which allows two players to play the game together even if one of them does not have a copy of the game. The game is temporarily downloaded to their system, allowing them to play until the connection is lost or ended. The mode can also be played by one player alone. The only pinball table that is compatible with this mode is Magmoor Caverns.

The object of a Wireless Mission is to score 100,000 points before the opposing player(s). To score points, the pinball must be launched and hit ramps, rollovers, spinners and saucers, among other objects. Stringing together combos allows for even more points to be scored. A leaderboard keeps track of the highest scores among Pinball players.

During the game, a Progress Bar keeps track of the players' progress, using blue markers to represent opposing players, and orange to represent the players on their DS consoles. The first player to reach 100,000 points wins. Hitting certain targets will allow the player to perform the Tower Jump, and shooting all Drop Targets will send Metroids to the table of an opponent with a higher score.

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