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Rabbit leads a mission to capture some Ninja Monkeys using traps made of sticky tree sap, but Skunk and his friends can't resist playing with the stuff. They get so sticky that they're barely able to fight off the attacking Ninja Monkeys. Before long, both the animals and the Ninja Monkeys are stuck together in huge, dueling sap balls. However, when Baboon gets caught in the huge sap ball, having been searching for the monkeys, Skunk and his friends find themselves in huge trouble as they battle to stop Baboon and the Ninja Monkeys.
After Baboon's Ninja Monkeys manage to fail to invade the Valley yet again much to Baboon's own personal dismay and frustration, Rabbit, fed up with Panda's teachings which demonstrate patience, decides to starts his own Kung Fu school with cool-colored belts, and Skunk is faced with a choice: stick with Panda or go to Rabbit's school. He ends up going to both schools as a student, and everything is fine until a tournament pits the best students from each school against each other, and now Skunk has to fight himself.
Impressed by Dr. Turtle's humorous bedside manner, Skunk resolves to become a comedian. His comedic styling comes in handy when he tags along with Fox and Rabbit on a special mission.
While Panda and most of the inhabitants of the Valley are away, examining a catapult that Baboon and the Ninja Monkeys have assembled, Skunk, Bird, and Ox are hanging around, guarding the Valley but things change when the Ninja Monkeys launch an attack.
Rabbit teaches Skunk how to sound tough, which leads to a muscle flexing contest with Baboon.
When Skunk's Green Tea Cake is stomped on by a Ninja Monkey, Skunk embarks on a quest of revenge with Rabbit assisting Skunk while also trying to stop Skunk from exacting his revenge against the Ninja Monkey responsible. However, when Rabbit and Skunk are captured and brought before Baboon, the two must find a way to escape.
Digging a tunnel to Dragon's lair (with the help of Rabbit) seems like it'd be tons of fun for Skunk. However, he quickly founds out that this is not the case because Rabbit is extremely bossy.
Skunk and Tiger venture into Dragon's territory so they can find an extremely hard walnut so that they can beat Pig at a game of Chinese Conkers.
Ninja Monkeys attack the Valley and they appear to be invisible to all except Ox. When Ox and Skunk save the day, however, Ox loses his ability to see them.
In exchange for a break from Panda's grueling training, Skunk journeys to The Hill of Moons deep in Dragon's territory to retrieve some of his master's favorite plums. Fox, Rabbit, and Tiger worry about Skunk, and they decide to follow him. Skunk soon finds himself fighting for his life when he's ambushed by Baboon and the Ninja Monkeys.
Skunk would like nothing more than to join Rabbit on night patrol, and Rabbit would like nothing more than to be left alone, so he scares the daylights out of Skunk with a story about a phantom Rooster who haunts the forest. To exact revenge Skunk and Tiger make a Rooster costume and in turn scare Rabbit from his post. But now with no one on patrol, it is up to Skunk defend the Valley.
When Skunk has nightmares of being controlled by Dragon and the Ninja Monkeys, Skunk and Panda must enter the dream realm to stop them.
Skunk quickly makes friends with a firefly and ask Panda if he can keep him as a pet.
Skunk wants to use Dragon's stolen magic jewel to help the Valley animals. However, Dragon has different plans.
After Pig has fallen into the enemy's hands and is suffering from amnesia, Pig thinks he is a Ninja Monkey. Skunk, Rabbit, and Praying Mantis must now find a way to return Pig to normal.
Skunk is forced to watch Turtle on a snow day. This is easier said than done, however, because Baboon and his Ninja Monkeys decide to steal Turtle's shell.
Truffles are in season, and their aroma transforms Pig into a truffle-seeking Mr. Hyde maniac. But Dragon wants the truffles for himself, in order to make a scale-soothing lotion that would set him free from his icy cave. Skunk and Rabbit attempt to protect Pig and his truffles from Dragon's henchman.
When Panda tests Skunk with the "box in paw" trick (Skunk has to snatch a pebble out of Panda's paw before he closes it), Skunk gets frustrated and storms off, almost walking into a net trap laid by Baboon and his goons. Unfortunately, Fox is caught but she doesn't lose her cool. In facing down Baboon, she teaches Skunk that sometimes patience and cunning can be much more effective than speed and strength.
Wanting Skunk to quiet down so he can get some sleep, Panda trains Skunk in a completely fictitious and very silent technique of transferring one's chi into a rock. But when the Ninja Monkey's swipe the rock that Panda just transferred his chi to, Skunk and Tiger hunt the chimps down to save Panda.
When Skunk accidentally breaks an ancient lantern that has hung in the Valley for hundreds of years, he blames it on the Ninja Monkeys. And he gets off scot-free. But soon everyone starts blaming the Ninja Monkeys for everything! And then no one seems particularly concerned when Skunk tries to warn them of a real monkey invasion.
