Brainiac's Ship is an interstellar warship commanded by Brainiac.
- On the right side of The Bridge, a transition can be performed that will send the opponent crashing through Brainiac's ship into space. One of the tentacles of his ship is bringing them back into Collection Room.
- On the left side of the Collection Room, a transition can be performed that will send the opponent flying. He/she got attacked a tentacle and brought it up to The Bridge.
- At the end of Multiverse Ladders, you face Brainiac on the Skull Ship. The villain gets extra moves, such as having tentacles come out of the ground.