Chapter 2 takes you to the mysterious Boggly Woods and the Great Boggly Tree, home of the Punies. Here, you'll meet your third partner, Flurrie, and encounter the X-Nauts for the first time. The chapter involves navigating a dark forest, solving puzzles within the Great Tree, and protecting the Punies from the X-Nauts. You'll need to guide a large group of Punies through various obstacles, utilizing their unique abilities. Be prepared for battles against X-Nauts and their robotic minions. Flurrie's wind ability will be essential for revealing hidden passages and blowing away obstacles.

While Paper Mario focuses on managing a crowd of Punies, Mario & Luigi: Dream Team similarly utilizes large groups through its Luiginary Works mechanics during 2D segments.