In the game, after Bowser kidnaps Princess Shroob, who was disguised as Princess Peach, he accidentally falls into a Time Hole and appears on Thwomp Volcano, where he jumps inside the volcano and appears in Thwomp Caverns. Baby Bowser also falls here after getting blasted out of Yoshi's Island.
Baby Bowser and Bowser start fighting with each other while Mario, Luigi, Baby Mario and Baby Luigi climb Thwomp Volcano and jump inside it to get to Thwomp Caverns with help from Mr. Thwomp. The Mario Brothers then descend down the caverns on a Thwomp Elevator to reach Bowser and Princess Peach, although a few times the elevator is unable to move downwards, caused by colored blocks blocking its path. Mario and co. go through the area, and hit the small blocks which make the big colored blocks disappear, then allowing them to continue downwards. After a while the Mario Brothers reach Bowser and Baby Bowser. A boss battle starts, and after Mario and Company defeat Bowser and his baby counterpart, and are about to save Peach, the Shroob Mother Ship comes and sucks Mario, Luigi, the babies and Peach in, and the U.F.O. leaves. Also seen after defeating Bowser and his younger self is a cutscene where Baby Bowser and Bowser land on the elevator, and it shoots upwards, making Bowser fall into the time hole far below that Mario and co. came out of to enter the stage, and Baby Bowser remains on the Thwomp Elevator, but it gradually begins to fall back down and hit the top of the Shroob Mother ship in which Princess Peach, Mario, Luigi and the babies are soon trapped inside of.
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