An airship carrying a young girl, Sheeta and her abductor, a secret agent working for the government named Muska is attacked by the air-pirate Dola and her sons in search of Sheeta's crystal amulet. In the resulting struggle, Sheeta falls from the airship, slowed by the amulet mid-fall. Floating safely down to a small mining town, she is discovered by a boy named Pazu, who takes her into his home to recover. On waking, Sheeta is surprised to find that Pazu is building a small aeroplane, with the intention of finding the lost city of Laputa, as his father had taken a photograph of it while flying. She tells him that her family lived in a small valley to the north named Gondoa, and that she had lived alone once her grandmother had died, until being abducted by Muska and his agents. Later in the day they are pursued by Dola's pirates, and later by Muska's soldiers. Eventually, the two fall into an abandoned mine, where they encounter the local eccentric 'Uncle Pomme', who informs them that Sheeta's amulet is one of the 'volucite' crystals formerly used to keep Laputa aloft.
Upon leaving the mines, Sheeta reveals her full name of 'Lusheeta Toel Ul Laputa'; whereupon they are captured by Muska, and when Pazu tries to defend Sheeta from the soldiers, he is knocked out in the process, and are taken to the fortress of Tedis; Pazu is imprisoned in the fortress' dark, cold and damp tower while Sheeta is imprisoned in a more lavish room. Later, Muska shows Sheeta a dormant Laputan robot and reveals his knowledge of her secret name, which he interprets as that of a Laputan royal line. Muska then threatens to have the military kill Pazu if Sheeta refuses to cooperate. In order to prevent this from happening, Sheeta orders Pazu to leave for his own safety. Distraught, Pazu returns to his own house, only to be dragged forcibly inside the house by Dola's sons and tied up. After being questioned harshly and rudely, Dola explains to Pazu that Sheeta was forced to tell him this in an effort to protect him. She also explains that once Muska has what he wants from her, he will most likely kill her. Upon hearing that airship Goliath will be taking off with Sheeta to find Laputa, Dola and her sons prepare to intercept and capture the crystal. Pazu asks Dola to join her pirates to save her. Dola initially refuses, but, after a moment of thought, reluctantly accepts and cuts Pazu loose and immediately leave for the fortress of Tedis. Sheeta, retained by Muska, recites an apotropaic verse and unexpectedly activates the amulet and the robot, who proceeds to destroy the fortress, while Pazu and Dola's pirates embark in winged 'flaptors' to rescue Sheeta themselves. Meanwhile the robot seizes Sheeta, but when struck by Muska's artillery, retaliates against the fortress, until Sheeta orders it to desist, losing her amulet in the process. The robot is then overcome by Goliath, and Pazu rescues Sheeta, while Muska obtains the amulet.
The pirates, accompanied by Pazu and Sheeta, return to their airship Tiger Moth, where Dola assigns Sheeta to the galley and Pazu to assist her engineer, and in which they pursue the direction identified by Sheeta's amulet as that of Laputa, while Muska follows in the same direction in the Goliath. Both airships arrive at Laputa on the following day, where the two children, separated from Dola's pirates, discover a city devoid of human life, but possessed of a park-like woodland with a gigantic "Eternal tree of life", maintained by a robot resembling that of the fortress. Muska's soldiers plunder the city's treasures, holding Dola's pirates captive, with the intention of having them lynched. The ancient city is revealed to be twofold; a crumbling, overgrown yet beautiful ruin of a castle above, and a perfectly preserved scientific marvel below, utilizing the ultimate evolution of the crystal levitation technology displayed by Sheeta's amulet, as well as holography, magnetic cohesion, pseudo-nuclear weaponry and a veritable army of the semi-sentient robots. Upon gaining entrance to the city's central sphere, Muska captures Sheeta and his agents open fire upon Pazu, receiving a scratch to his left cheek; whereupon Pazu frees Dola's pirates and pursues Muska.
In the center of Laputa, containing the immense 'volucite' crystal keeping the city aloft, Muska identifies himself as "Romuska Palo Ul Laputa", another royal line, and uses Sheeta's "key" crystal to access the advanced Laputian technology. He then destroys the soldiers and the "Goliath" outside; whereupon Sheeta seizes her crystal amulet and flees, prompting him to pursue her. Encountering Pazu through a gap in a wall, Sheeta gives him her amulet, and is herself later cornered by Muska in Laputa's abandoned throne room. Arguing with Muska, Sheeta realizes and explains that the people of Laputa left the castle because it had no life. Muska refuses to believe her and shoots off her two pig tails, threatening to shoot her ears as well unless the crystal amulet is given to him. Pazu then enters and says he'll give the crystal amulet to Muska if Pazu can talk to Sheeta; Muska grants the two one minute to negotiate. Sheeta and Pazu then recite a "Spell of Destruction', blinding and killing Muska and destroying much of the city. Having survived the collapse, Pazu and Sheeta re-unite with Dola and her pirates (who have had the presence of mind to swipe some of the city's treasures before fleeing), and later part from them to fly to Gondoa as Pazu had promised, whereupon the ending credits show the remains of Laputa still aloft, with the guardian robot still tending the garden, maintained by the volucite crystal embedded in the roots of the central tree, in high orbit above the earth.
|Characters||Original Japanese Cast|| 1989 English Dub Cast|
| 1998 English Dub Cast|
(Lusheeta Toel Ul Laputa)
|Keiko Yokozawa||Lara Cody||Anna Paquin|
Debi Derryberry (young Sheeta)
|Pazu||Mayumi Tanaka||Barbara Goodson||James Van Der Beek|
|Captain Dola||Kotoe Hatsui||Rachel Vanowen||Cloris Leachman|
(Romuska Palo Ul Laputa)
|Minori Terada||Jeff Winkless||Mark Hamill|
|General Muoro||Ichirō Nagai||Mike Reynolds||Jim Cummings|
|Uncle Pom||Fujio Tokita||Ed Mannix||Richard Dysart|
|Takuzō Kamiyama||Barry Stigler||Mike McShane|
|Yoshito Yasuhara||Dave Mallow||Mandy Patinkin|
|Sukekiyo Kamiyama||Eddie Frierson||Andy Dick|
|Boss||Hiroshi Ito||Clifton Wells||John Hostetter|
|Old Engineer||Ryūji Saikachi||Eddie Frierson||Matt K. Miller|
|Okami||Machiko Washio||Lara Cody||Tress MacNeille|
|Madge||Tarako||Barbara Goodson||Debi Derryberry|