Darkseid attacks the planet Earth, destroying a military base in the process. The player takes control of a member of the Justice League of their choosing, and tracks down the other members for information, only to be attacked by them. As the hero defeats the other Justice League members, they discover that they are android duplicates. Coming to this conclusion, the hero battles Cheetah and Despero for more information.
They both lead the hero to Darkseid, who then forces the hero to fight their duplicate. Upon defeating the clone, the hero must face Darkseid himself. After the hero defeats him, the other League members are freed, and the military base is restored.