The Brainiac Skull Ship is Brainiac's personal flag ship from within which he conducts and oversees his various mastermind plans.
Shaped in the motif of a skull, the Skull Ship originated from a time when Brainiac was imprisoned within the core of a computerized prison world. Gaining control of the planet's systems, he managed to cause the system's sun to go supernova. Following the destruction of his physical form, he was able to use the planet's resources to create a new body and a "Skull Ship" for himself to use to escape the facility.
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- Brainiac keeps his collection of Bottled Cities on board the Skull Ship where he can observe and study them at his leisure.