Three hundred years after six men crash-landed from space on an uninhabited planet named Terra II, six cities have developed (one for each of the original founders). Genetic engineering assured the survival of the race, as every man raises clones instead of children from natural propagation. Unable to genetically engineer women, however, has resulted in a planet of men and their android servants called marionettes, all of which take female form. But suddenly, out of happenstance, a local boy, Otaru, from the city of Japoness awakens a special marionette named Lime from a secret underground capsule. Lime has the ability to laugh and get angry and demonstrates amazing strength - attributes that make her unlike any other marionette. But more importantly Otaru and Lime become friends.

The Imperial Guards of Japoness fear that evil despot Faust, leader of another city called Gartlant, is up to something dreadful. Three of Faust's special marionettes, termed Saberdolls, suddenly appear in Japoness and destroy a group of secret agents that previously burned down resident fancy boy Hanagata's house. The Saberdolls then disappear just as nimbly as they arrived. Even though Hanagata annoys Otaru, Otaru still fights to save Hanagata's little brother from the flames. But civilians impede Otaru's would-be rescue, claiming the cause hopeless. In an act of valor, Lime saves the boy, leaving the others to question the differences between man and machine.

Furor Faust, spurting Hitler-like slogans, plans to attack Japoness. Meanwhile, Otaru, Hanagotta and Lime take a tour of the national museum in Castle Japoness. When Lime accidentally breaks a national treasure, Imperial Guards race after the trio. Otaru sacrifices Hanagata to the mob in order to escape with Lime, but they end up in a secret room that houses the Shogun, Japoness' leader. Just as the Shogun starts to enjoy their company, and alludes to knowing more about Lime's origin, one of Faust's Saberdolls, Panther, disobeys Faust's orders and appears to eliminate the Shogun. Lime battles with Panther, but both are on equal footing and are getting nowhere. In the melee, Otaru accidentally awakens another special marionette, Cherry. With Cherry's help, they defeat Panther, who returns to an angry Faust and is punished for disobedience. Otaru, now with two devoted and human-like marionettes, walks home.

Cherry is in love with Otaru, but every time she gets close enough for a kiss, Lime interferes. After defeating average street thugs in a fight, Cherry solicits their help in a faux kidnapping plan designed to get Otaru alone. Otaru responds to Cherry's "ransom" letter and quickly goes to an abandoned warehouse to rescue Cherry. But when Otaru's moment of triumph comes, dangerous smugglers appear at the warehouse.

The Shogun sends for Otaru, Lime and Cherry and explains why the two marionettes are different than others - they each have a special maiden circuit that gives them emotion. Unfortunately, the secret to making maiden circuits was lost long ago. But just as he's about to explain Otaru's role in the mystery, an android replica of Faust flanked by Saberdolls appears to learn the secret himself. Once he does, the android explodes, wounding the Shogun. As the Saberdolls attack and Lime and Cherry defend, Otaru frees another marionette with a maiden circuit, Bloodberry. Another marionette has joined Otaru's family.

Bloodberry, also attracted to Otaru, takes a more forward approach to love. But after Otaru refuses her forward advances and marriage proposal, she decides to woe him by making his greatest wish come true. Bloodberry mistakenly thinks that Otaru's wish is to fly, so she makes a flying machine and they fly away, much to Otaru's fright and dismay. They crash land on Mt. Kamuna where the evil beast Ponta lives. Lime, Cherry and Hanagata assemble flying machines of their own for rescue.

With three marionettes to feed, Otaru finds that his financial means have rapidly dwindled to one remaining coin, enough for one day's supply of rice. Otaru sends Lime to get the rice, but she returns with a lottery ticket instead, having been tricked into believing it a magical piece of paper. When Otaru's idea of running a burger stand ends up costing more than it profits, their only hope remains in the lottery ticket. Luckily Otaru and company win the "happiness is yours" prize - unluckily the prize is a year's supply of pickles.

Hanagata, now Otaru's annoying neighbor, has finally decided to declare his love for Otaru, but just as he attempts to do so, marionette collectors kidnap Lime, leaving Otaru devastated and in no mood to listen to Hanagata's declaration. Spurned, Hanagata peevishly tells Otaru that his feelings for the marionettes are unnatural. But Otaru ignores the jibe, saves Lime and insists upon caring for each marionette as if they were human.

Faust makes his move and overthrows another of the six cities. Intent on ruling all of Terra II, his next target will be Japoness unless someone can break into the heart of Gartlant and destroy the main computer. Otaru agrees to take on the secret mission issued by the Shogun's council, not for patriotism, not for honor, but for the fame associated with being a hero. He's a sucker for trading cards in candy boxes. But when Lime learns that war makes you lose people, she decides to go on the mission alone. Fortunately, Hanagata informs Otaru, Cherry and Bloodberry in time for them to reach Lime in an underground passageway just as she needs help fighting Faust's Saberdolls.

After Otaru, Lime, Cherry, Bloodberry and Hanagotta successfully repel the Saberdolls, they journey into Gartlant to detonate the central computer. Cherry plans for Lime, Bloodberry and Hanagata to distract the city's guards while she and Otaru hack into the main computer room and place explosives on the central computer. The plan appears to work until, in the midst of their escape, Otaru and company find themselves surrounded by the Saberdolls with deactivated explosives in hand.

In the midst of Saberdolls, Otaru and gang look defeated until a young boy named Micky rescues them by blinding the Saberdolls with flash pellets. Resolved to make Gartlant a better place and save Japoness, Otaru and friends trek once again to the main computer room, this time through another series of abandoned tunnels. Before Otaru can enter the computer room and complete his mission, however, he has an urgent need to relieve himself, which similarly spurs the need in Hanagata. But as their golden arches fall into the computer room, the Saberdolls catch up.

Upset and jealous that Otaru kissed one of the Saberdolls, Luchs (in an attempt to distract her during the effort to destroy Gartlant's central computer), Lime, Cherry, Bloodberry and Hanagata make for poor companions on the trip back to Japoness. When they happen upon an abandoned spa resort, Otaru resolves to take a break and enjoy the facilities to ease the group's tension. When a plasma tornado develops over the resort it suddenly becomes clear why the spa resort had been abandoned, and why Lime, Cherry and Bloodberry abruptly malfunction. Otaru builds an iron "lightning" rod to attract the plasma tornado away from the resort, kisses each of the ill marionettes goodbye, and plans to sacrifice himself to the tornado by making sure the rod stays in place.

After saving it from Gartlant, Japoness gives Otaru and ganga a hero's welcome. Otaru gets an agent and abandons himself to a lifestyle filled with fame and fortune, ignoring his marionettes, who decide to leave Otaru. But fame has taken its toll on Otaru and he realizes just in time how much he misses his marionettes.

Constantly fighting over who is the most deserving of Otaru's affections, Lime, Cherry and Bloodberry enter a marionette contest designed to honor the best marionette on Terra II. The Saberdolls, Panther, Tiger and Luchs, are also ordered to enter the contest disguised and seduce Otaru to Gartlant's side. The Saberdolls make a mess, however, and Otaru's marionettes soon discover their true identities.

The Shogun summons Otaru, Lime, Cherry and Bloodberry to the Pioneer Museum where Lime first awakened. He tells Otaru that the maiden circuits not only make emotion possible, but they allow the marionettes to grow and develop like human beings. The Shogun explains that, in accordance with this extraordinary feature in the maiden circuit, it will soon be necessary for Otaru to revive the human female for humans to continue to survive on Terra II. Otaru questions what the Shogun means, and how he can accomplish such a task just as military agents from Gartlant set the museum on fire. Lime, Cherry and Bloodberry save Otaru and the Shogun from the flames, but they are unable to save what the Shogun most cherishes - the picture of a girl named Lorelei.

The marionettes learn about life and death when Lime adopts a squirrel for a pet. As Lime nurses the squirrel back to health, and then chooses to set the squirrel free for its own good, the marionettes experience new emotions, proving that their maiden circuits are continually growing, just as the Shogun said they would. When the Shogun hears of the pet project that the marionettes have undertaken he is pleased because the growth signifies one step closer to reviving females on Terra II.

Lord Faust gives the Saberdolls one last chance to wreak havoc on Japoness before casting them out forever. This time the Saberdolls do not fail. They slip in to kill the Shogun while an unidentifiable huge black machine (also sent by Faust) distracts Otaru, Lime, Cherry, Bloodberry and Hanagata. Suddenly, as the machine is poised over the city, Cherry recognizes that it's a huge bomb. Faust's command holds the key to Japoness' survival.