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Super Mario World
The Koopa Clown Car first appears at the end of Super Mario World in the final fight with Bowser. Bowser hovers in it above the top of Bowser's Castle in the Valley of Bowser. During the fight, Bowser will unleash an improbable amount of Big Steelies and Mecha Koopas. After jumping on a Mecha Koopa, Mario can pick it up and throw it at Bowser, damaging Bowser.
After a few hits, Peach emerges from the Koopa Clown Car and gives Mario a mushroom and is soon pulled back into the Koopa Clown Car. Following this, Bowser will attempt to use the Koopa Clown Car to crush Mario as well as shoot fire balls at him. During this time, the car's face grows angrier and angrier looking.
Eventually, the Koopa Clown Car and Bowser are defeated. Peach emerges safely and Bowser is dropped from the car.
Super Mario RPG: Legend of the Seven Stars
In the opening scene of Super Mario RPG: Legend of the Seven Stars Bowser once again kidnaps Peach in the Koopa Clown Car. He can also be seen using it when Mario arrives at Koopa's Keep to fly to the top.
The car is once again seen in the ending. A Shy Guy rides inside while Bowser and his troops repair the damage done by the Smithy Gang. It makes a final appearance in the parade at the end of the game as part of a float in the appearance of Koopa's Keep with Croco and his bandits attempting to loot it. Bowser from within the Koopa Clown Car gives chase until Booster hijacks it from him.
During the events of Paper Mario, Bowser uses a gigantic stone version of the car to lift Princess Peach's Castle into the sky. This version has a cameo in the Rainbow Road course in Mario Kart: Super Circuit.
In addition to the new version, the traditional car appears at the beginning of the game as Bowser invades Star Haven as well as Peach's castle. He uses it to escape after Mario defeats him.
Also of note, the platform used by Bowser to power himself up during his final battle against Mario resembles a long, flat version of the Koopa Clown Car, while several smaller versions of the Koopa Clown Car can be found in the hangar of Bowser's Castle.
In the Super Mario World cartoon episode "Send in the Clown", Bowser uses the Clown Car to travel above Dome City, advertising the "circus" he has set up at his castle. Later in the episode, Bowser uses the Clown Car to battle Mario, the same way he does in the game. In "Rock TV", the Clown Car reappears in the background, housing a potted plant.
In the Subspace Emissary mode of the Wii game Super Smash Bros. Brawl, the Clown Car appears twice. The first time Bowser uses it to escape with the Princess who isn't rescued from Petey Piranha. The last time it is used to escape from Falco, Donkey Kong and Diddy.
Multiple minigames in the upcoming Mario Party 9 feature this car.
In addition to appearing in Brawl, it was a trophy in Super Smash Bros. Melee.
Bowser's single-seat, personal airship doesn't exactly handle like a dream, but it wasn't designed to be sporty. The Koopa Clown Car was made to carry Bowser's huge weight,not to mention a logic-defying arsenal of massive bowling balls. In Super Mario World, Mario busted the Koopa Clown Car by pelting it with Mecha Koopas.