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Challenge is a multiplayer mode in Metroid Prime: Blast Ball, and the separate Blast Ball mode of Metroid Prime: Federation Force. It is a co-operative mode in which a group of players, and/or computer-controlled Mechs, work together as a team to fight increasingly difficult waves of enemies across five matches of Blast Ball. The enemy players are divided into Alpha, Beta, Gamma and Delta Squads, and an "Elite" team. Challenges are balanced towards a full party, and can be incredibly difficult if playing alone.

Completing a Challenge successfully will unlock a random Paint Job, as well as the Hyper Mode MOD, an unbreakable MOD that can be used in the Campaign. A slightly altered version of the Federation Force credits will play the first time a Challenge is completed. Completing 10 Challenges will unlock another Paint Job.

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