Space Strikers has a single continuous plot running through all twelve episodes. The universe is inhabited by humans and a variety of other space-faring species. They are under threat from the mostly-robotic armies of Master Phantom, a human cyborg who believes Captain Nemo left him to die. Earth and multiple other planets have already been conquered at the start of the first episode. Members of various other species join the human crew of the Nautilus to fight back, including an anthropomorphic wolf, an anthropomorphic dolphin, a Cupid-like creature, and a variety of robots. Due to their previous friendship and shared academy training, Captain Nemo and Master Phantom attempting to outwit each other is recurrent theme in the show.