Puni

The Punies are a species of small quadrupedal creatures which resemble insects found in the game Paper Mario: The Thousand-Year Door. They live in The Great Tree located in the Boggly Woods. Mario must use them to defeat a rival clan, the Jabbies, twice in The Great Tree.

Story
As Mario was exploring Rogueport Sewers for the first time, looking for The Thousand-Year Door, he stumbled upon a small insect creature which was, indeed, a Puni. However, it escaped through a small opening, and Mario was unable to interact with it.

Later, after Mario gets the first Crystal Star (the Diamond Star), he goes back to Rogueport Sewers, now with a new ability, which is turning sideways. Luckily for Mario, next to the opening in which the insect had gone through were bars. Mario went through these bars to find out that the insect was just behind them. Mario learns that this insect is named Punio, who tells Mario his homeland, Boggly Woods and primarily The Great Tree, is under attack, and that he needs his help.

The Great Boggly Tree
When Mario reaches The Great Tree through a "secret entrance", he is told by a few Punies, which were all hidden, that their friends have been locked up somewhere in The Great Tree. Upon freeing them, Mario and all the Punies in The Great Tree will attack the Jabbies, the Punies' rivals, who have allied with the Secret Society of the X-Nauts. A total of 101 Punies, including Punio and Petuni, will temporarily join Mario during the events of Chapter 2.

After Mario defeats Lord Crump and the X-Nauts, the Punies will go back to their normal lives, and even make peace with the Jabbies.

Trivia

 * The word "Puni" is a pun on the word "puny", meaning "small".
 * In Super Paper Mario, Francis keeps posters of Petuni in his house, giving the Punies a cameo appearance.
 * The way Mario leads the Punies in Chapter 2 is very similar to the game Pikmin. Like the Pikmin, the Punies will follow Mario everywhere, but they can scatter and depart from him if and when they get distracted. Also, Mario needs a certain number of them to activate some switches, which is also hinting at Pikmin, where Olimar needed at least a certain number of Pikmin to solve some puzzles. Finally, the glowing antenna the Punies sport on their heads mirrors both the Pikmins' stems and the antenna on Olimar's helmet.
 * Toadette seems to love Punis, according to the quote on the back of the Rogueport news board at chapter three, which says, "I miss those little Punis. They are so mushy and adorable".
 * Because of there being 101 Punies in all, that Mario has to rescue, this could be a parody on the story about the 101 Dalmatians. The Punies do also look a little similar to dalmatians, although it's only Punio and Petuni which have darker spots.
 * It is possible to have some Punies outside of the cage after it falls. What must happen is to get some Punies separated from Mario before the Puni Orb is placed on the pedestal.