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The Ship Guardian seeks to defend Brainiac's ship and sends legions of underlings to try and stop the player-created hero or villain from disabling Brainiac's main weapon and thus destroying the ship that is containing them.
When the weapon is destroyed Brainiac Ship Guardian attacks the hero or villain personally and sacrifices itself in defense of the now doomed ship - moments after the Brainiac Ship Guardian is destroyed either Lex Luthor or Superman teleport into the scene to help the hero or villain escape to safety.