Chapter 2

The second Crystal Star is revealed to be in The Great Tree, home of small creatures known as Punies, deep inside Boggly Woods. When searching for the pipe leading to Boggly Woods in Rogueport Sewers, Mario and his partners encounter Punio, who tells them that the X-Nauts have invaded the Great Tree, capturing most of the Punies and that the Jabbies, the Punies' enemies, have allied with the X-Nauts and are trying to expulse the Punies from the Great Tree. Mario and co. decide to help out the Punies, and therefore Punio leads the group to the Boggly Woods. After getting there, Mario and co. encounter the Shadow Sirens with a necklace, who do not recognize him due to having lost a sketch of him. The group continues and arrives to the Great Tree. However, they realize that the tree is locked. Punio suggests they find Madame Flurrie; to find the secret entrance. However, upon reaching her home, Flurrie reveals she has lost her necklace and doesn't want anyone to see her without it. After defeating the Sirens and returning the necklace to Flurrie, she joins them in their quest. The group finds the secret entrance and enters the tree; after freeing the locked Punies with the aid of a special orb and after solving the Great Tree's puzzles and defeating the Jabbies, they get the second star at the bottom of the tree. There, Lord Crump snatches it, and activates a time bomb to blow up the tree. After chasing him to the entrance, he stops the bomb and uses Magnus Von Grapple to fight the heroes, but he is defeated by the group. Afterwards, the X-Nauts evacuate the tree and Mario and co. obtain the Emerald Star.

At the X-Naut headquarters, the X-Nauts inform Sir Grodus that Mario has taken the Emerald Star. Meanwhile, TEC-XX calls for the Princess, and asks her to dance with him. TEC then lets Peach e-mail Mario.

Bowser can be seen arriving in Petalburg, and then talking to what he thinks is Peach, but is revealed to be a poster by a nearby Koopa.

As Mario and his team move on, they receive another e-mail from Peach, who tells them that the X-Nauts are searching for the Crystal Stars. Mario and his team reveal the location of the next Crystal Star, and they visit the Prof. for details.