Editing Mega Baby Bowser

After dispelling four of the Wonder Wool, Mega Baby Bowser staggers back and his Wonder Wool float off the screen again. In [[Easy Mode|Mellow Mode]], this is the only portion of the battle where Mega Baby Bowser drops [[Heart (item)|hearts]]. He starts over, this time throwing six giant black yarn balls into the air. More yarn balls rise into the air than the ones he threw. These yarn balls are even bigger than the ones prior to this, and they destroy much of the tower's terrain. Only the three darker black sections of the parapets and the cannon bobbins remain, though the black yarn balls land in neat stacks of three. The stacks are positioned in the same six way split the earlier yarn balls had. One larger yarn lands in the center of each space, while the other two land on top. They lean on the remaining blocks and the blocks holding up the cannon bobbins. Each stack of three has one yarn ball of a non-black color land on top, which did not appear with the earlier rising yarn balls. The black yarn balls never have bows appear. To finish the battle, Yoshi has to attack the remaining four Wonder Wool, while noting that Mega Baby Bowser's hand attack now knocks away the primary ground of the battle, leaving behind [[pit]]s. It does not have this effect on the lowest and centered yarn ball of every stack, which makes for additional safe space that is uncomfortably close to the pits. There is also no space to crouch under the fire breath attack, requiring that Yoshi quickly unravel a colored yarn ball or have Baby Bowser knock part of a stack away to create room should that be the player's decision on how to dodge. When the yarn balls on the tower run low, Mega Baby Bowser can again replenish them, this time throwing both black and non-black ones while summoning more.

In the [[Boss Tent]], Baby Bowser's Boss Challenge also includes Mega Baby Bowser, fought directly after normal Baby Bowser. There is no checkpoint in this version; dying while fighting Mega Baby Bowser means starting from Baby Bowser again. While the cutscene of the transformation is skipped, Yoshi's yarn balls are still lost in the transition. Mega Baby Bowser's speed increase while fighting him in the Boss Tent makes him substantially more difficult to fight. It is harder to run away from his attacks and access the Wonder Wool close to his back. Also, the rate Yoshi can unravel one of the yarn balls in the battle remains constant despite the increased attack speed from Mega Baby Bowser, leaving Yoshi very vulnerable while obtaining big yarn balls. Instead of the ending cutscene playing out, Yoshi's position is reset using a fade to black for the victory dance.