Several years after the events of Leroy & Stitch, Stitch has since left Lilo and Kauai and is flying around space on a jet scooter he stole from Jumba, going back to his old destructive programming. Jumba attempts to recapture his genetic experiment but the two get caught in a wormhole. Jumba crash-lands his ship on an asteroid in one of Saturn's rings where he finds Pleakley, who has been stranded there as well. Stitch, meanwhile, crash-lands back on Earth, finding himself on an Okinawan island named Izayoi. He goes around the island searching for food, but then 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, Jumba and Pleakley manage to escape Saturn and find their way to Izayoi Island, reuniting with Stitch. The two decide to stay with the experiment and his new friend, and Jumba ends up making a bracelet called the Good Deed Counter in order to track Stitch's deeds along the way.

Hämsterviel tries to take Stitch's good deed counter by controlling Sparky.

As Yuna and Stitch decide to make a wind chime for Gramma's birthday, Stitch is visited by and reunites with Angel. Yuna tries to get Stitch and Angel involved with making Gramma's present, but she is soon left to make it herself. After Angel sings her siren song to Stitch with a croaky voice, he becomes enraged and causes chaos around the town, eventually breaking the wind chime Yuna made for Gramma. Yuna then blames Angel for "ruining everything" since she arrived, leading Angel to leave in disgrace. After Jumba finally returns Stitch to normal, Stitch and Yuna start to worry after Gramma gives Stitch a note from Angel that reads "Goodbye". After searching around but failing to find her, Kijimunaa reveals he found her and is taking care of her, as she's suffering a head cold. After getting better, Angel finally helps make Gramma's present. Angel then leaves on a cruise ship, waving goodbye to Yuna and Stitch.

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. Felix cleans up messes all around the island's town, but he starts cleaning away antiques when he runs out of trash and messes to clean.

Yuna's student Taro doesn't like eating healthy food to win the black belt competition. When Reuben comes, he makes rice balls 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.

Penny shows off a book of her idol, Tetsuo. So Yuna and Stitch pull Penny's book and Stitch tears it up in half. Meanwhile, in Yuna's dojo, directors and producers come and pick Stitch to become an actor.

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 Gramma 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 Kijimunaa, Yuna and Stitch set out to find her. They find her fallen into a deep coma, and 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 Hämsterviel and Gantu, too.

Hämsterviel gets Jumba to absorb power from the Spiritual Stone so he can gain ultimate power, while Yuna plans to break a shrunken-down Stitch out of the American football-shaped container Hämsterviel put him in.

When Hämsterviel escapes from prison, he gets a small flying insect to turn Stitch's good deed counter the opposite. Whenever he does a good deed his points go down on his good deed counter and when he does bad things his good deed counter goes up. When Kijumunaa gets really sick, Stitch decides to get rid of his good deed counter and save him along with Yuna. Jumba tries to figure out what's wrong with the good deed counter and Pleakley finds the bug that reversed the good deed counter. Hämsterviel sends Gantu to try to take the Spiritual Stone.

Pleakley's parents bring Mr. Stenchy to the island when they come to visit. The little pink experiment causes a really bad aroma on the island and Stitch gets jealous of his cuteness once again.

Experiment appearances: Experiment 254 (Mr. Stenchy), Skunkuna (a skunk-like experiment made by Dr. Hämsterviel)

On Halloween, Yuna and Stitch meet the son of the famous vampire Dracula, Count Dracula Junior, who goes around Izayoi eating everyone's trick-or-treating candy.

Experiment appearances: Experiment 010 (Felix), Experiment 221 (Sparky), Experiment 624 (Angel), Experiment 625 (Reuben)

A new girl named Sasha, who is a fashion model, comes into town, causing a rivalry between Yuna and Penny to see who's a better fashion model.

Yuna tells Stitch the story of Captain Khan, so Stitch decides to find the pirate and his ship. However. Yuna, Stitch, and Kijimunaa run into a group of young pirates who are looking for the ship as well, so Stitch decides to tag along with them.

Reuben brings Checkers to Izayoi, and the latter experiment turns Penny into the queen of the island. However, she soon grows tired of controlling everyone and wants Checkers to get off her head, but he refuses to do so. Stitch, who is unaffected by Checkers' powers but gets turned into a living pineapple thanks to a brainwashed Jumba, seeks Reuben's help to remove Checkers from Penny's head and stop her reign, using an incredibly spicy sandwich to get him to come off Penny's head on his own.

Experiment appearances: Experiment 029 (Checkers), Experiment 625 (Reuben)

Hämsterviel re-evils some experiments using a recording of Angel's siren song and causes them to do chaos again, disrupting a class project at Yuna's school to build a playground for an upcoming festival. Link binds Yuna and Penny together, and Babyfier transforms everybody else (apart from Stitch) into tiny babies. While Stitch takes care of the babies, Yuna and Penny must try and co-operate together to find the antidote to get everyone back to normal.

Experiment appearances: Experiment 033 (Hammerface), Experiment 151 (Babyfier), Experiment 251 (Link), Experiment 319 (Spike), Experiment 507 (Woody), Experiment 625 (Reuben)

Yuna gets a keychain from Sasha, but it begins to fall apart, so she tries to hide it from the latter. Shortly afterward, a chicken shows up with a clothespin that was blown of Officer Suzuki's clothes line, which Stitch, Jumba, and Pleakley mistake for being the keychain and chase after it. Hämsterviel notices this from his lab and believes that the clothespin is a key to unlocking the Spiritual Stone, so he decides to go after it by riding a robotic Pteranodon to the island to retrieve it.

Experiment appearances: Experiment 625 (Reuben)

It's Christmas time, and when Gantu accidentally sends Experiment 267 (Wishy-Washy) instead of Experiment 297 (Shortstuff), Stitch decides to use Wishy-Washy's ability to grant people's wishes to raise up his good deed counter. However, Yuna wants to get something for Gramma, but she tells her she doesn't need to get her anything. When Penny kicks Ted out of her entourage, he wishes he could ruin Penny's Christmas party and Wishy-Washy accidentally turns her Christmas tree into a monster, and with no more wishes left, Stitch and the others must save Penny.

Experiment appearances: Experiment 297 (Shortstuff), Experiment 267 (Wishy-Washy), Experiment 625 (Reuben)

Stitch and Taro accidentally disturb a yokai and switch bodies.

Dads Day celebrations are coming up at school, but Yuna believes that her father, who is still away and busy with his research on sea slugs, will not show up. Stitch arranges to have Yuna's father arrive on the island and meets him on his ship. Meanwhile, Hämsterviel decides to use a climate-changing machine under the water near the island to cause a powerful storm so that he and Gantu can steal the Spiritual Stone unopposed. Discovering Hämsterviel's machine, Yuna's father and Stitch take a submarine to destroy the machine and save the ocean. In the end, Yuna finally reunites with her father, just in time for Dads Day.

Experiment appearances: Experiment 625 (Reuben)

Because her mother died when she was a baby, Yuna does not remember her face. On a certain night, Stitch finds out, and Experiment 276 (Remmy) entered Yuna's dreams and turns it into a nightmare. Stitch, Jumba, and Pleakley rush after 276 to get Remmy out and save Yuna. Ultimately, Remmy is captured and he allows Yuna to see her mother's face.

Experiment appearances: Experiment 276 (Remmy)

Experiment 303, Amnesio, comes to the island and starts taking peoples' memories.

Experiment appearances: Experiment 025 (Topper), Experiment 303 (Amnesio), Experiment 383 (Swirly), Experiment 390 (Slimy), Experiment 502 (Yang), Experiment 602 (Sinker), Experiment 603 (Zap), Experiment 608 (Slugger), Experiment 619 (Splodyhead), Experiment 625 (Reuben)

Stitch accidentally upsets Angel when he trips and drops a Valentine's Day cake on her. Desperate, Stitch uses Hunkahunka to have her fall in love with him unconditionally. His plan works, but things soon get out of hand, as Hunkahunka starts randomly tapping people.

Experiment appearances: Experiment 323 (Hunkahunka), Experiment 624 (Angel), Experiment 625 (Reuben)

Posing as a human duke, Experiment 627 tries to take Angel away from Stitch. This is all the doing of Dr. Hämsterviel. However, when Stitch and Angel are almost crushed by Hämsterviel's ship, 627 saves them.

Experiment appearances: Experiment 624 (Angel), Experiment 625 (Reuben), Experiment 627

A gallery is opened at the hotel Penny's father manages, but a masterpiece is stolen. Stitch imitates a TV detective to find it.

Yuna's father returns to the island, but he isn't acting himself. Stitch finds out it's a tanuki pretending to be him and tries to show Yuna the truth.

"A Little Hämster Love": One of Hämsterviel's schemes unintentionally ends up making him out to be a hero to the islanders.

Experiment appearances: Experiment 625 (Reuben)

"Pleakley Loves Hollywood": An alien director comes to the island and decides to make Pleakley a movie star.

Experiment appearances: Experiment 221 (Sparky), Experiment 254 (Mr. Stenchy)

Hämsterviel uses Swirly to try to get Stitch to use his wish to make Hämsterviel the ruler of the universe. ^[4]

Experiment appearances: Experiment 383 (Swirly), Experiment 625 (Reuben), Experiment 617 (Plasmoid), Experiment 619 (Splodyhead)

Yuna's mean, bullying cousin Tigerlily (Zuruko) arrives on the island and moves in with her, Stitch, and Gramma. She uses her beauty and fakes kindness to manipulate others. Meanwhile, Hämsterviel plans to use Welco's bubble powers to send Stitch out into the ocean and drown him.

When Nosy appears on the island, Yuna attempts to use him to reveal her cousin's cruel nature (as no one believes her). But despite her best efforts, everything keeps turning in her cousin's favor. ^[5]

Hämsterviel kicks out five of the weaker experiments and they find their way to Earth. However, Hämsterviel needs them back when it is discovered they stole a treasure chest containing a big secret of the tiny genius.

Jumba, Stitch, and Tigerlily are shrunk by Jumba's first experiment, Shrink. The latter two decide to play some pranks around the island, while Hämsterviel and Gantu go after the shrunken Stitch to crush him.

Bonnie and Clyde show up and cause trouble, so Stitch makes himself into a superhero character he calls "Stitchman" to stop them.

Stitch and Yuna are sucked into an alternate universe by Experiment 272/Wormhole and meet an evil Stitch with a jetpack who enjoys destroying an abandoned city, along with alternate versions of Jumba, Pleakley, and Gantu. As Yuna tries to convince the alternate universe's 626 that ʻohana is better than destroying things, the Jumba of Yuna and Stitch's universe tells them via her good deed tracker communicator that they only have a limited time to find the interdimensional portal back home or they'll be stuck in the alternate universe. However, only Wormhole knows where the portal is and he refuses to leave until he finds a slipper belonging to Jumba that he lost to a previous portal before, which he believes to be in this alternate universe.

Stitch and his friends are going to Tokyo Disneyland, with Yuna's father, Jumba, Pleakley, and Penny. ^{[7] [8] [9]}

After finding out that Tigerlily is afraid of lighting, Stitch and Yuna chase a cloud to try and capture Raijin's son, also named Raijin, from it, but he's small and not very scary. Stitch tries to scare Yuna's cousin again but fails, and so does the yokai, so Jumba creates an electric energy drink using Sparky's electricity, which Stitch uses to temporarily gain electricity powers.

All the people are scared of pollution in the sea, so Stitch has to defeat Ploot in order to save it.

Stitch is hired by the Grand Councilwoman to save the universe from an evil experiment named Cyber. Last episode of Stitch! ~The Mischievous Alien's Great Adventure~.

Kijimunaa's sister, Kijimaggie, who looks like him and is pink, visits Izayoi. She worships her brother, believing him to be brave and strong, not knowing how cowardly he is. Her belief is shattered when Kijimunaa is unable to destroy a meteor hurtling towards Izayoi and Stitch does so instead, saving the island. Kijimunaa then finds a strange but hurt living plant on the ground and plants it; noticing his kindness, Kijimaggie's faith in him is restored. What they don't know was that the plant is actually an offspring of Jumba's Experiment 509, Sprout, who was on the meteor that Stitch destroyed, and soon the "Sproutling" grows big and aggressive. Other Sproutlings grow all over the island, strangling everyone with their vines. Stitch tries to stop the Sproutlings by uprooting the main one, but even he is unable to. Kijimunaa notices a tear at the base of the main Sproutling's stem and cries over it, causing one of his magic tears to fall into the tear, healing the Sproutling, returning him to his original size, saving everyone, and causing Kijimaggie to see him as a hero again.

Stitch and Yuna move to Newtown with Tigerlily as the behest of Gramma due to (in the Japanese original only) Izayoi Elementary School closing soon. While there, they meet Dolores, Jessica, her friends Toriko and Makiko, and Hiroman. Later, Stitch wants to return Yuna's handkerchief, but ends up almost destroying the school, which upsets Yuna. Meanwhile Hämsterviel, on orders from his new partner, Lady Delia, has recaptured the other experiments and begun mutating them with additional abilities. His intent is to capture Stitch so Delia can extract the Neo-Power Chip from within him. Stitch later begins to leave and gets attacked by Plasmoid and Splodyhead, and again destroys the school, which then makes Yuna think Stitch has broken his promise and lied to her. Stitch stays away from Yuna to try to catch the two altered experiments, but gets captured by Gantu. Yuna feels guilty for not believing Stitch and goes to find him at school, but then gets attacked by Plasmoid and Splodyhead. Stitch then saves Yuna and she apologizes to him for not believing him. After hearing about Hamsterviel's failure, Delia tortures him with a bomb.

Yuna continues to try to be Jessica's friend with little progress. However, Yuna has to come to the rescue when Hämsterviel modifies Sample with the ability to control his victims with a powerful melody.

Yuna is trying to attend Jessica's birthday party in another attempt at befriending her, but Jessica invites Yuna only to humiliate her and have her clean up before and after the party. Hämsterviel is inspired by this and outfits Wrapper with the ability to trap his enemies in indestructible gift boxes.

Hiroman's team is going to be on TV, and everyone's getting excited about the event. While trying to return some things, Yuna learns the soccer captain is blackmailed by his sisters, who are Tigerlily's old friends. Meanwhile, Gantu gets the wrong experiment and Dorkifier is released on the town, sticking people including Stitch, Yuna, Hiroman, and Pleakley in ridiculous outfits. Hiroman's so upset with his new look he doesn't want to come out.

Yuna's class heads off to camp where she volunteers to help out with the haunted trail in order to spook Jessica. She gets some extra help from Delores, Stitch, Jumba, and Pleakley in doing so. However, Gantu's not too far behind with both Toons and Spooky in hopes of catching Stitch.

The whole town's excited over a local limited-time-only dessert called fluffy rolls. However, Stitch's cousin PJ is given a Stitch costume and starts framing Stitch for a variety of pranks.

While Delia is away, Hämsterviel decides to compete in a child prodigy show on Earth for the big cash prize alongside Reuben and Gantu. Also competing for their school are Jessica, Yuna, and Delores. Realizing the competition is fierce, Hämsterviel decides to cheat with Spike's help.

Gantu and Reuben trick the kids into going to a deserted island to find a flower said to grant wishes. Only they find Sprout, now upgraded with 627's DNA.

Stitch and Yuna go back in time to the day Jumba built Stitch.

Yuna, Stitch, and Pleakley have messed up the timeline by traveling to the past and Jumba must finish building Stitch before it is too late.

Stitch, Yuna, and a mass number of other students go to an amusement park created by Hämsterviel called Wishlanda, where they have nothing but fun and their every wish gets granted by a disguised Wishy-Washy. However, those who visit become too exhausted to do anything, allowing Hämsterviel to possess them using their "point badges".

Stitch and Yuna find a mysterious yellow alien flutist, who quickly gets everybody's collective attention. What nobody realizes is Flute (named Bragg in the Japanese original) is actually Experiment 145 (misnumbered 021, the number of "Twang", in the Japanese original), who not only frames Stitch for mass destruction but the more attention he gets, the stronger Flute becomes, even to the point where he can outdo Stitch.

While setting up a Halloween party for the school, Jessica becomes possessed by the experiment Witch, turning her into a literal witch.

Hämsterviel disguises himself as a substitute teacher to get close to Stitch, also becoming the coach of the school's 5th grade girls' volleyball team. The only problem is that he's starting to like the job and becomes invested in the team's upcoming game against the 6th grade team.

Yuna has to do a report on shoguns and what they eat, so she borrows Toons to bring a picture of a shogun's dinner to life, only to bring an actual shogun to life. Not only does she have to hide him, Tigerlily falls for the shogun and Hämsterviel decides to upgrade Kixx with a katana.

Yuna gets turned into a dog by a transmutated Elastico. Mistaking Yuna's dog form as a stray, Jessica takes her home in the latest attempt to date Hiroman, prompting a rescue from Stitch.

Toriko, the tall girl of Jessica's group, signs up for a teenage beauty contest alongside Jessica. Feeling crushed, she accepts Yuna's help in the event. However, Hämsterviel, having bad memories about Homecoming, sends down a stronger Thresher to wreck the show.

Hämsterviel gives Reuben an upgrade, in hopes he'll capture Stitch. But problems arise when Reuben's more interested in Angel.

Stitch plans a Christmas party and invites Yuna's father and grandmother to New Town to surprise Yuna. Meanwhile, Hämsterviel gives out clones of Mr. Stenchy and Mrs. Sickly out as presents as part of an evil plot.

Stitch and Hiroman swap bodies. While the two enjoy being each other, Hämsterviel sends down Heat ^[i] to capture Stitch in Hiroman's body.

Tired of being Hämsterviel's errand boy, Gantu tries to strike out on his own, losing five experiments in the school. However, Stitch is hit by both Retro and Shrink, turning him into a giant version of his old self.

Reuben pretends to be Angel and invites Stitch and friends onto a cruise ship where Hämsterviel plans to throw Stitch overboard so he can catch him without resistance.

While taking Yuna to school, Stitch spies someone who appears to be Lilo. Both Pleakley and Jumba are unconvinced as Lilo was starting college when they last spoke. While seeing Stitch happy with this girl, Yuna learns of how Lilo and Stitch broke up. Pleakley explains that Stitch went on a four-year mission and Lilo went to college with the promise that they would meet when they returned, but Lilo didn't. Seeing the confusion, Hämsterviel uses Morpholomew, now with the ability to transform himself into any picture the experiment sees to capture Stitch. While trying to rescue Stitch, Yuna discovers the girl Stitch has been following is actually Ani, Lilo's near-identical daughter. After stopping Gantu, Stitch learns that the reason Lilo didn't show up was that Lilo's sister Nani had given birth at the same time as their meeting, and the two make up after years apart.

Hämsterviel sends Babyfier to turn Stitch into child so Stitch would be easier to catch. Instead, Babyfier turns Yuna and her classmates into kids. With Tigerlily more preoccupied for an upcoming date, Stitch is running himself ragged keeping the kids in check.

It's Valentine's Day and everyone goes to a chocolate factory where Angel is performing. After the concert, they all go and make personalized chocolate valentines, but Hämsterviel is scheming to use Fudgy, now outfitted with the ability to grow after eating chocolate.

It's Yuna's birthday, but she thinks everyone has forgotten...even Stitch! While preparing Yuna's surprise party, Stitch falls asleep and Hämsterviel sends Remmy to trap him in his own dreams, causing Stitch to fall ill.

Checkers escapes Hämsterviel and runs amok at Yuna's school, causing the students to fight for the power to control everyone.

Jumba has developed a second and stronger Power Chip, one stolen by Delia. To test it, Hämsterviel uses it on Dupe so each duplicate made is stronger than the last. Stitch decides to use Dupe so that he can get out of his chores and trouble ensues.

Delia finishes making a new experiment who is stronger than Stitch named "Dark End". Dark End and Stitch battle, leaving Stitch unconscious.

Taking place before the events of "Boss" and "Dark-End", Ace appears to save the day and Stitch decides to help him. However, Ace's relentless and restless heroism causes him to develop back and body aches, depleting his powers and confidence.

To confront a planetary war at the sand planet of Katuna, Stitch must leave Yuna and Earth behind.

Yuna goes missing and Stitch goes on a desperate search to find her. This episode was first announced on Stitch Day 2015 (June 26).