In the pilot episode, after the events of Leroy & Stitch, Lilo is now an adult and she has a boyfriend and a daughter, making Stitch to leave Hawaii and blast off into space after stealing a Jet Scooter, while acting totally nuts and goes back to his old programming ways of destroying things. An attempt to recapture Stitch is made, but he makes an emergency landing on Earth. Stitch finds himself on an Okinawan island to search for food and go back to Hawaii and tells Lilo he's sorry for running away from home but instead he meets a young girl named Yuna. After bonding during a storm, the two become friends.

Stitch is told of a legend that will grant him any wish that he wants, an Okinawan legend; but all the while, he has to help apologize for the damage he caused in Chitama Town with Yuna. All the while, Stitch tries to land a Good Deed by getting back a letter from Yuna's father, whom she discarded with haste. Later, he then runs into Jumba and Pleakley whom stay with him upon landing in Izayoi Island; and Jumba ends up making a bracelet called the Good Deed Counter, in order to track his deeds along the way.

Obaa tells Stitch and Yuna of a powerful spirit named Kijimunaa, who they go on an adventure to meet.

Yuna is upset when her classmate Piko draws a bad picture of her. After trying to make her smile and failing, Stitch tries to cheer her up by drawing pictures of her smiling, but does so all over the house. She demands he cleans it but he instead runs off to the beach where he unknowingly picks up the magical tail brush of Muun, who lost his brush as he swung it round saying he had lost his desire to draw. Stitch being angry about Yuna draws a picture of himself in the sand and is shocked when it comes to life! The giant Stitch drawing then goes on a rampage, and even against Stitch's best efforts, it manages to grab Yuna. Muun appears and tells Stitch to draw the smiling Yuna again using his brush, who when made soothes the Stitch drawing and saves the real Yuna. Finally, Muun gets his inspiration back for painting.

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Yuna and Stitch decide to make a wind-chime for Obaa's birthday. Stitch then gets a letter from Angel telling him she's coming to the island. As Yuna tries to sort out their present, Stitch reunites with Angel, even showing her the spiritual stone. Yuna continues to try to get Stitch and Angel involved with Obaa's present, asking them to help her design it, but Yuna is soon left to make it herself. But after Angel sings to Stitch with a sick/croaky voice, Stitch reverts back to being bad. He starts to cause all sorts of chaos around the town. He eventually goes too far by breaking the wind-chime Yuna made for Obaa, which Yuna then blames on Angel, upsetting Angel so she leaves. After Jumba finally gets Stitch back to normal, Stitch and Yuna start to worry after Obaa gives Stitch a note from Angel that reads "Goodbye" After failing to find her, they head home sorrowfully when Kijimuna reveals he found her and is taking care of her. After getting better, Angel finally helps make Obaa's present. Angel then leaves on a cruise ship, waving goodbye to Yuna and Stitch.

Stitch accidentally hatches a baby bird who thinks Stitch is its mother.

Yuna wanted to take a picture of Stitch using her grandma's camera, but it is out of film. So, she take Jumba's camera to take a picture of Stitch. Tarou sees all the pictures of Stitch, but he sees that Stitch is blinking animatedly in the picture. Then, many copies of Stitch came out and invade Izayoi. They stole cameras and making camera stew, saying "Camera!" many times. So Stitch has to put down many copies of him.

Stitch is scolded by Yuna for making a mess. Rather than clear it up himself, he borrows a transmitter and calls in Felix to help.

A yōkai named Warracchi starts playing harmless and amusing pranks on the island's inhabitants. Seeing how happy the jokes seem to make everyone happy, Stitch soon begins playing pranks of his own, but they quickly get out of hand.

Yuna has a class visit to the pineapple factory. Yuna was late because Jumba invented a good deed memory to let Yuna type her diaries. But Stitch looked at the pineapples, he was coming to invade the factory. Then, a blue slug (which is one of the Izayoi spirits) attacked the pineapple factory. Jumba invents an electric gun to shoot the blue slug.

Yuna gets sick on the day of a festival and Stitch goes with Angel instead. Stitch meets a yōkai named Dolores who promises to make fireworks for Yuna in exchange for her own things.

Christmas is coming to the island. Hamsterviel has a plan to hypnotize all the kids of the island to do his bidding by eating evil cookies. Jumba comes up with a plan to reverse the attack. After Yuna and Stitch stop him they don't think there's gonna be a Christmas. When Santa comes he gets Stitch to help him send the presents around the island.

Yuna's student Taro doesn't like eating healthy food to win the black belt competition and when Reuben comes he makes riceballs with secret food in it so Taro can win.

Yuna and Stitch meet a Feebema named Damacchi who doesn't fit in with other Damacchis. They soon realize the reason he doesn't belong is because he's a meteor shower.

When a student at Yuna's dojo wishes his father wasn't so strict, a yōkai named Himamushi makes it come true. Yuna and Stitch try to convince Himamushi to change him back to normal.

Piko shows off her book of her fan, Kid Cop. So Yuna and Piko pull Piko's book and Stitch tears up into half. Meanwhile in Yuna's dojo, directors and producers came, and picked Stitch to become an actor.

Yuna, Taro and Stitch enter a singing competition but Stitch realizes he can't sing. Taro really wants to win so he can get a trip to the hot springs for his dad, so Pleakley gave him lessons.

While the postman is sick, Yuna and Stitch deliver a dropped letter to a woman named Mrs. Tanaka. Meanwhile, Jumba and Pleakley find a letter for Yuna.

Jumba gets Stitch to be his new lab assistant but when Stitch doesn't help properly he quits and runs into town. Jumba notices some mystery things going on in town and meet a yokai named Topsy-Turvy who turns things around.

Everyone is planning a surprise party for Yuna and Stitch promises not to lie to her after he lies for eating her corn and Yuna thinks no one cares about her.

Yuna, Stitch, Jumba and Pleakley help Kijumnaa go to the Twin Caverns so he can become a guardian and help Obaa get better.

Yuna and Stitch discover that there`s a treasure buried in the forest of Shadow Valley, Angel appears and decides to go with them. But when Obaa tells them the horrible legend of the yōkai Pilolo who lives in the forest they decide not to go. But the treasure dwells on Angel`s mind and she sets out to find it on her own. With the help of Kijumnaa Yuna and Stitch set out to find her. They find her fallen into a deep coma, they must now find out why.

Stitch is captured and now the whole island must rescue him. His friends, Jumba, Angel, Sparky and Felix are brainwashed by Hamsterviel and Gantu too.

Hamsterviel gets Jumba to absorb power from the spirit tree so he can gain ultimate power and Yuna plans to break Stitch out of prison.