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.

Skunk can't stop his constant giggle fits. This isn't easy, however, because Panda takes him on a secret spy mission.

Skunk somehow manages to get Rabbit's Ninja Monkey workout dummy mask stuck to his own face. Before he can eep "no", Skunk is swooped up into a Ninja Monkey unit and is face-to-face with Dragon himself.

Skunk spies Panda practicing a legendary Kung Fu move that freezes one's opponent called the Divine Hand. Of course, Skunk uses the move to prank everyone in the Valley. But the joke is on him when the Ninja Monkeys watch Skunk showing the move to Rabbit. Now Skunk and Rabbit have to freeze all the Ninja Monkeys before they can pass on the secret technique to Baboon.

When Ninja Monkeys have entered Rabbit's borrow, Skunk invites Rabbit to stay with him and Panda. But soon he becomes a total pest.

Dragon gives Baboon the power to use the "Jinx's Palm": a one-shot deal where whoever is struck with his blow is saddled with horrible bad luck. His target: Panda. But when he strikes Skunk instead, Skunk finds a way to use his terrible luck to his advantage by wreaking havoc on the Ninja Monkeys. Baboon then tries to stop him by using the "Fortunate Palm", a good luck remedy, in an epic clash of good and bad luck, pitting Skunk and Baboon against each other in a battle where luck will decide who the ultimate victor is.

As endurance training, Panda has Skunk place an egg between his legs and hold it there – without breaking it – until Panda returns and says it's okay. Problem is, Panda is quietly kidnapped by the Ninja Monkeys. Skunk is determined to pass the test and hang onto the already rotten egg, which makes the rescue mission all the more difficult.

After checking out a piece of Baboon's fur (which Rabbit got from his most recent encounter), Skunk and Rabbit find the secret to a forgotten fighting move known as "The Lighting Claw" but the two find themselves in a whole heap of trouble when Baboon gains access to the move.

The kindhearted Skunk takes in a Ninja Monkey who was kicked out of Baboon's army. But Panda thinks that that monkey is a spy. Skunk figures out that the Monkey is not telling the truth and tricks him into telling Baboon that they are planning a massive attack.

After Baboon gets banished by Dragon for an embarrassing defeat, Snake starts a rumor that Skunk invented a powerful new move.

Rabbit convinces Skunk to go with him on a "dangerous mission" but truthfully, he just wants to retrieve stolen poems he wrote about Fox which soon becomes intense when Baboon and the Ninja Monkeys arrive.

Skunk is too embarrassed to admit that he plays with ants. However, it turns out to be very useful when Baboon attacks the Valley with an army of red ants.

The Ninja Monkeys accidentally shrink Baboon using a powerful new potion and Baboon takes full advantage of the situation by pretending to be Skunk's "inner voice", causing Skunk to rebel and go against his friends.

Skunk wants to help Turtle with his New Year's kite display. But soon, he thinks it's a good idea to infiltrate Baboon's great wall.

Skunk pretends to be sick so he can get out of doing Panda's chores. However, he soon feels guilty when all his friends go into one of the big battles.

Realizing how powerful Skunk's stink is, Rabbit makes a task force to collect it and use it as a weapon.

When Panda hears that Baboon's making a bigger army, he has the women of the Valley (Duck, Crane and Fox) train Skunk in the art of fan fighting. Skunk thinks it's cool at first but Rabbit and Pig soon tease him for the "girly" style of fighting.

Skunk invents a new move, The Dizzy Master, making enemies unable to hit him. Such a discovery makes him believe he is unstoppable so he and Pig go off to steal Dragon's beard in order to prove it.

Panda makes Skunk take cooking lessons from Duck but as soon as he masters it, the Ninja Monkeys have taken an extreme liking to their cooking so much that they've become too blotted to do much of anything, much to Baboon's disgust and annoyance.

When Baboon uses his new cannon to attack the Valley, Rabbit ignores Panda's orders for a defensive plan to make an even bigger weapon.

Panda tries to teach Skunk a skill that would make him heavier. But when Skunk struggles learning it, he uses a giant boulder in its place.

Baboon challenges the Valley animals in a gaming event, but it becomes serious when Skunk unintentionally wagers the Valley.

Skunk, Pig, Ox, and Bird try to mimic the elders' tea ceremony, believing that it gives them powerful skills.

Skunk and Pig are informed by Tiger, Snake, and Fish about an initiation chamber that makes one become a true warrior. All three claim they have already succeeded in doing this, but eventually they reveal to each other that neither of them completed the initiation.

Panda tries to teach Skunk art, but he fails at every form. But when Skunk learns that getting beaten up by Ninja Monkeys turns his abstract sculptures into beautiful and realistic works of art, he takes full advantage.

After another plan of Baboon's goes horribly wrong, he blames it on the Ninja Monkeys and fires them, going to great lengths to eject them from the area. They start to move into the Valley and take up Skunk, Bird, and Ox's private spots. Now they have to make it look like they were defeated by the monkeys, so Baboon can take them back but with Rabbit insisting on fighting the Ninja Monkeys as a means of strengthening himself, it might be not an easy task for Skunk, Bird, and Ox to accomplish.

When Turtle's notebook is stolen by the Ninja Monkeys, Snake goes on a special mission to get it back. Wanting to prove that he can be a good spy, Skunk invites himself to join Snake.

Panda teaches Skunk to see without seeing, which Skunk finds silly. But when he gets lost in a tunnel made by the Ninja Monkeys, Skunk has all-new respect for sound.

Baboon disguises one of the Ninja Monkeys as a female skunk in order to capture Skunk for Dragon's birthday. But Skunk "saves" the decoy, and takes her to the Valley. Skunk is happy to meet another of his kind, but all his friends keep getting in the way of his romance.

Panda has Skunk learn underwater combat from Fish. It's a good thing too, because Baboon has built a dam in the river causing a drought.

Tired of all the chores that come with his "destiny", Skunk makes a deal with Mantis to trade lives. But he soon becomes bored and all the missions Mantis is now tackling all end up going horribly wrong.

Rabbit, Fox, and Skunk alert Duck that Panda has been captured by Baboon. Rabbit tells the story from his point of view, while Fox recounts the story of Panda's capture from her point of view, but when she fails to explain it in a manner Duck can understand, all hope lies in Skunk's side of the story.