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 in fact android duplicates. Coming to this conclusion, the hero battles Cheetah and then Despero for more information.
They both lead the hero to Darkseid, who then forces the hero to fight their own 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.
Justice League Task Force received mostly negative reviews. The four reviewers of Electronic Gaming Monthly scored the Genesis version a 5.875 out of 10, criticizing the choppy animation, limited number of moves, and most especially the poor controls, which they said made executing special moves "too much work to be any fun."GamePro gave negative reviews to both the Genesis and SNES versions, similarly citing poor controls, unimpressive special moves, and sprites which look good in still frame but ugly in animation.