The inside of The Great Tree is also pretty massive. There are many rooms that can be accessed using Warp Pipes. Down below, there is also a hidden Item Shop that can be accessed using Flurrie's ability. There are also jail cells at the very top of the tree where the X-Nauts kept most of the Punies locked up in.
Mario and his friends head into The Great Tree after learning a Crystal Star is located there. Punio leads them there but the front door has been replaced by a metallic one that is already locked. Punio remembers of a secret way to get inside but they must have Flurrie. Mario and the others then come back with Flurrie and she uses her wind powers to reveal the secret passageway and head inside. However, Mario soon finds himself fighting a couple of X-Nauts and defeats them in battle. Mario quickly learns that the X-Nauts are also after the Crystal Star and tries to find a plan. Punio also notices that most of the Punis are gone and urges Mario to try and free the Elder first. Mario heads upward and finds all of the Punis locked up in cages. The Puni Elder is locked up by herself in the red cell and the majority of the Punies, including Punio's sister, are locked up in the blue cell. Mario then heads into the next room and finds Ms. Mowz near a knocked out X-Naut. She tells Mario that she is just looking for some more rare badges and tells Mario that the Crystal Star is, indeed, located somewhere in the tree. As Ms. Mowz leaves through the window, the X-Naut wakes up and attacks Mario thinking he was the one that knocked him out. Mario defeats him in battle and retrieves the Red Key. Mario and Punio unlock the red cell but the Puni Elder yells at them for not freeing the others. After a long story, the Puni Elder entrusts Mario and Punio with 10 Punies and must use them to free the others. Mario, Punio, and the Punies all head downward to try and find the Blue Key to free the rest of the Punis.