Bowser first encounters The Tower of Yikk while he was searching for the first Star Cure when he was on his way to Dimble Wood to confront Durmite to whom he doesn't know who is in his body. Bowser then takes advantage by sneezing, due to a pollen allergic reaction. It activates its propeller and makes it come to life, then crushes Bowser with his giant leg and Mario and Luigi must go to the Rump Command and spike and spark his energy so that Bowser can turn big and battle the Tower of Yikk. In this battle, Bowser realizes that The Tower of Yikk's body is too hard and sees that its head is its weak spot and to punch its head, he has to punch it into the river to make him attack its weak spot temporarily.
After defeating it, Bowser enters the tower and sees Yikk who tells him to check out the Boo-ray Machine he created and Bowser checks it out and flashes a light through his stomach so that Mario and Luigi can continue their chase with Durmite.