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The Great Tree is a giant tree in Paper Mario: The Thousand-Year Door. It is located in Boggly Woods and is the home of the Puni Tribe. There is actually a secret entrance in the Great Tree that Mario must go through to get inside, seeing that the main entrance is locked. However, the secret entrance is anything but secret as it is labeled "Secret Entrance" and is surrounded by flashing lights.

The Emerald Star is located within the tree. As such, Lord Crump and his X-Naut troops invaded the place to find it, even if that meant teaming up with the Jabbies (the rivals of the Punies), and additionally, imprisoning the Punies. Punio enlisted the help of Mario, Goombella, Koops, and Flurrie to liberate the Punies, take down the Jabbies, retrieve the Emerald Star, and drive the X-Nauts out of the Tree. Mario also obtained the Super Boots while he and his friends were here. After Mario and his friends find the Emerald Star, Crump steals it and activates a 5-minute self-destruct mechanism. Soon Mario, Goombella, Koops, Flurrie and the Punies corner Crump and demand that he surrenders the Crystal Star and leave the tree forever. However, instead of surrendering, Crump deactivates the detonator and summons his robot, Magnus Von Grapple and attacks. After defeating the robot, Crump and the X-Nauts are driven out of the tree and Mario is given the Emerald Star as a reward.

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