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Darkseid attacks the planet Earth, destroying a military base in the process. A member of the Justice League (that the player chooses to play as) tracks down the other members for information and aid only to be attacked by those heroes in their related locations.
As the hero defeats the other JL members, they deduce that the others aren't the real leaguers, but rather android clones. Coming to this conclusion, the hero battles Cheetah and then Despero for more information.
After the hero defeats him, the other League members are freed, and the military base is restored.