Meanwhile on Earth, Stitch is still not fitting in and causes another disaster. Lilo tries to encourage him by saying he's one-of-a-kind, comparing him to Frankenstein. Naturally, that just makes him feel worse. Suddenly, a crash is heard from below. Running downstairs, the pair encounters Gantu, breaking into their home. In the ensuing chaos, Stitch thrusts his belly out at Gantu, only to be blasted into a net. Gantu finds and takes a blue pod with the number 625 on it before abducting Jumba for interrogation. Lilo and Stitch manage to take Jumba's ship to chase Gantu into space and engage him in battle, before being defeated and falling back towards Earth.
Back at the house, Lilo, Stitch and Pleakley find the container Jumba was hiding. Pleakley realizes that these are the other 625 experiments, in dehydrated form. He warns them not to tell anyone or put the experiments in water. Deliberately disobeying Pleakley, Stitch and Lilo retrieve the container and hydrate Experiment 221, who promptly escapes.
Meanwhile, Jumba is being held captive on the ship of Dr. Hämsterviel, who is surprisingly a small gerbil/poodle/rabbit-like alien. Unable to intimidate Jumba, Hämsterviel activates Experiment 625, who has all of Stich's powers, to attack him. Fortunately for Jumba, while 625 has all of Stitch's powers, he is incredibly lazy, a terrible coward, and prioritizes in making sandwiches above all else.
Meanwhile, Pleakley is able to come into contact with Hämsterviel's ship via telephone. Hämsterviel tells Pleakley that he wants a ransom of the other 624 experiments in return for Jumba. When Pleakley informs the other family members what the ransom is, Nani proceeds to call Cobra Bubbles while Lilo and Stitch go out to find 221. When Cobra arrives the next morning, he seems to already know about what happened. Meanwhile, Lilo and Stitch finally catch a troublesome Experiment 221 at a hotel.
The rendezvous time arrives and Pleakley and Cobra show up with the container, not knowing that it contains only 623 experiments. Pleakley hands the container over to Hämsterviel, who is shocked to find that one is missing. Lilo then shows up with Experiment 221 trapped in a glass vase. Announcing that she has named it "Sparky", she says that Sparky is part of Stitch's, and thus her, ʻohana. Hämsterviel tells her to give him the experiment or Jumba will be shot dead.
After several moments of thinking and hearing Cobra, Pleakley, Jumba and Hämsterviel persuading them, Lilo and Stitch set Sparky free and break Jumba from his bonds. On Cobra's signal, the Grand Councilwoman's ship rises out of the nearby ocean and aims several guns at Hämsterviel. Lilo protests, saying that Hämsterviel has the other experiments and Sparky overhears.
Sparky proceeds to use his electrical abilities to blow the power on the Councilwoman's ship, while Hämsterviel and Gantu climb back aboard their own ship with the experiments. In a last attempt to stop Hämsterviel, Lilo and Stitch stow away on it as it leaves, with Sparky following.
Lilo and Stitch manage to swipe the container with the other experiments in it. The struggle for the container between Lilo, Stitch and Gantu results in releasing the dehydrated pods to rain down and scatter throughout Hawaii. Having captured the heroes, Hämsterviel tells his plans to clone Stitch a thousand times over and orders Gantu to do what he wants with Lilo. While Gantu puts Lilo in a teleportation pod to send her to an intergalactic zoo, Stitch is strapped to a weight just heavier than he can lift.
Watching as Stitch tries to avoid being vivisected by a laser for the cloning process, Sparky shows that he has reformed by causing the cloning machine to short-circuit. He then breaks Stitch free and the two strap Hämsterviel to the device before rescuing Lilo.
Having locked Hämsterviel in handcuffs, Lilo, Stitch, and Sparky short-circuit Gantu's ship, causing it to crash near a waterfall on Kauai, leaving Gantu humiliated. Landing Hämsterviel's ship back at the rendezvous point, they give Sparky a new home powering the Kilauea Lighthouse, which hasn't been running in years because powering it was very expensive. They then persuade the Grand Councilwoman to let them rehabilitate the other 623 experiments. The Councilwoman places Hämsterviel under arrest, and Jumba whispers to Pleakley that he has plans for making Experiment 627. At the end of the movie, Experiments 202, 529, 455, 489, and 390 are activated, thus leading to the series.
In a post-credits scene, Jumba and Pleakley hope to go home with the Grand Councilwoman this time, but they are left stranded once again.
- Daveigh Chase as Lilo Pelekai
- Chris Sanders as Stitch
- Tia Carrere as Nani Pelekai
- David Ogden Stiers as Jumba Jookiba
- Kevin McDonald as Pleakley
- Ving Rhames as Cobra Bubbles
- Dee Bradley Baker as David Kawena
- Kevin Michael Richardson as Captain Gantu
- Jeff Bennett as Dr. Jacques von Hämsterviel
- Corey Burton
- Zoe Caldwell as Grand Councilwoman
- Kunewa Mook as Hula Teacher
- Liliana Mumy as Mertle Edmonds
- Rob Paulsen as Reuben (Experiment 625)
- Frank Welker as Sparky (Experiment 221)
The film's original title was going to be Lilo & Stitch: A New Ohana. At some point, there was a decision to only have Stitch's name in the titles of both the movie and the subsequent series, which was planned to be called Stitch! The Series. Eventually, this was abolished, resulting in both this film and the series having mismatched names.
- Unlike the original Lilo & Stitch and the sequel Lilo & Stitch 2: Stitch Has a Glitch (released two years later), this film is rated G by the MPAA, making it the first film in the franchise to have been designated that rating.
- Without the credits, the film is only 57 minutes long.
- When Gantu blasts Stitch into a net, the net itself is green instead of red.
- Pleakley refers to the phone book he uses to look up some numbers in deep space as the periwinkle pages, an homage to the yellow pages.
- When the experiment pods landed on the island, Jam, Mary and Slimy's pods were red, and they were all labeled 455. But Digger's pod was purple, and Huggo's pod was green. These pods are supposed to correspond to the series number.
- There might be some trivia in the movie that Digger is supposed to be in the 1-series, and Huggo should be in the 2-series. But at the end of the movie, these pods were red, and they were labeled 455.
- During the scene where Stitch hot-wires Jumba's red spaceship, a shot of him from the rear shows his ears having the same notches (left lower; right upper) as though he was facing the camera.
- When Lilo climbs and falls over the fence into Mertle's backyard and crushes Mertle's tent, the flashlight she was carrying disappears. Then, when Mertle and her friends come rushing out of the tent, Mertle shines an identical flashlight on Lilo.
- On the film's VHS and DVD covers, Lilo's dress is colored green, while in the actual film, she does not wear green in any scene, just like in the other films.