Episodes center around the crew of the spaceship Nautilus, led by Captain Nemo, in an attempt to liberate Earth and other planets from the control of Master Phantom.
They are under threat from the mostly-robotic armies of Master Phantom, a human cyborg who believes Captain Nemo left him for dead.
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.
At various times in an episode, a small green icon appears in the corner of the screen to alert the viewer to put on 3D glasses.
Early 3D sequences typically feature repeated background and foreground images moving in opposite directions over the characters or ships on screen, giving the illusion of rotation or movement.