Mario and Luigi: Superstar SagaEdit
In Mario and Luigi: Superstar Saga. The Koopa Cruiser was use tranport Mario, Luigi and Bowser to the Beanbean Kingdom. After the battle against Fawful, Fawful summoned another Vacuum Helmet and used it to knock Bowser's Koopa Cruiser out of the sky. the Koopa Cruiser was then crashed down to Stardust Fields. The Cruiser (in a poorly-repaired form) was later used by Bowletta to capture Princess Peach, who turned out to be Luigi in disguise, although their attempt at doing so was unsuccessful as Luigi, stalling them with help from the Koopa Cruiser's Pinch Crane, managed to not only escape but also return the Beanstar to Beanbean Castle. It is unknown what happened to the Koopa Cruiser after the events of the game - it is likely it returned in Bowser's possession.
Mario and Luigi: Partners in TimeEdit
After Baby Mario defeats Baby Bowser The shroobs attack, and baby bowser calls Kamek to bring the Koopa Kruiser. In it some Hammer Brothers teach the babies some of their technuiqs. the koopa kruiser then stops at holijolli village in order to save the adult mario bros.. When atemting to go to shroob castle, Princess Shroob shoots a Shroob missile at it and it crash-lands in baby bowsers castle.