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The Mushroom Sea is featured prominently in the episode "Reptiles in the Rose Garden." At first, Bowser transports the White House (along with the President) to Dark Land so that Kootie Pie Koopa can rule the United States for her sweet sixteenth birthday. However, merely abducting the President isn't enough, so Bowser vows to send him where he will never be rescued: the bottom of the Mushroom Sea.
Using his Levitation Beam, Bowser lifts the White House off of the ground and sends it over the Mushroom Sea, where he releases it, letting it sink to the bottom. As the President is too busy talking on the phone to notice what has happened to his home, his wife fears for their lives, but there is nothing that she could do at this point.
Fortunately, Mario dons a Frog Suit and dives into the Mushroom Sea, dodging the Blooper Nanny, Blooper Babies, and the Jelectro that chase after him. Eventually, Mario makes it to the White House and is greeted by a shocked Mrs. President. However, Mario quickly assembles a pump out of pipes to flush the water out of the White House and raises it to the surface.
Later, after Mario and Luigi take control of the Doom Ship from the Sledge Brothers, Mario uses the Levitation Beam to lift the White House out of the Mushroom Sea and warp it back to Washington, D.C.
Although it is not mentioned by name, the Mushroom Sea is seen in two other episodes of The Adventures of Super Mario Bros. 3. In "Mind Your Mummy Mommy, Mario," Luigi, Princess Toadstool, and Toad escape from Castle Koopa on their Steam-Powered Mummy Sled and use it to ride across the Mushroom Sea.
In "Never Koop a Koopa," Luigi and Toad wait behind in a boat on the Mushroom Sea, while Mario and Princess Toadstool enter Castle Koopa. When Mario and the Princess don't return, Luigi and Toad dive into the Mushroom Sea and enter the castle through a drainpipe.