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While Punio was away in Rogueport, the X-Nauts attacked The Great Tree and imprisoned most of the Punies. Meanwhile, Punio met Mario in Rogueport. Mario proceeded to follow him to the entrance to Boggly Woods. Punio then took Mario to the Great Tree. When they arrived, they noticed a red door on the tree that was installed sometime while Punio was gone. Punio makes it very clear to Mario it had never been there before. Punio remembers a secret entrance that the Puni Elder notified him about sometime in the past. However, he has trouble finding it. He decides he must seek the aid of Madame Flurrie. When they arrive, Madame Flurrie is beside herself. She is overcome with distraught over losing her necklace. She is very taken by Punio's cuteness, however, but still refuses to help until they get her valuable jewelry back. After Mario defeats the Shadow Sirens, Punio, Mario and his party return her priceless necklace. She joins Mario's party and finds the secret entrance to the Great Tree. The secret entrance turns out to be just a small hole in the tree, which is obviously fit for a Puni. Punio enters the secret entrance and proceeds to open the red door, allowing access for Mario and his party. Upon their entrance, they find the Great Tree crawling with X-Nauts. None of the other Punis trust Mario, and believes Mario to be in league with the X-Nauts. Punio profusely and desperately plead with the other Punis to accept this "hairy old man", and they obstinately refuse to do so until the Puni Elder comes and chews them out. Mario, Punio and Mario's partners drive the X-Nauts out. Punio rescues his beloved sister Petuni and the Puni Elder and The Great Tree continue to live in harmony.
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