In an effort to rescue Cosmo the Seedrian from Bowser's forces, the Emerald Searches stow away on a Separatist transport ship en route to Arkham Asylum, which has been taken over by the Joker and his band of Gotham super-terrorists after getting rid of the Arkham staff. Now the only problem is: how do our heroes think they're going to escape and rescue Cosmo in time before the next batch of super-criminals arrive to check up on Joker's progress in locating another Chaos Emerald?

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