From the Super Mario Wiki
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The Star Cruiser is a ship built by the Star Spirits in Paper Mario. Mario and all of his partners use this ship to travel to Bowser's Castle. It docks inside the giant Bowser head in the front of the castle, which is a hangar for Bowser's Koopa Clown Cars. Mario can return back to the cruiser at any point and return back to Star Haven or even Toad Town.
The Star Cruiser later appeared during the parade when the player beats the game. All of Mario's party members can be seen in or around the vehicle.