Three hundred years ago, six men crash-landed on Terra II after their ship blew up. Through genetic engineering, men raise clones instead of children. Unable to clone women, society instead has female servant robots called marionettes who function on very simple AI. In Japoness, a young man named Otaru accidentally discovers a secret chamber in the abandoned pioneer musuem on the outskirts. Inside is a marionette like nobody has ever seen before...

Otaru struggles with Lime's unique personality, which his neighbors decry as a defective marionette. Meanwhile, Baikou and Tamasaburou of the Japoness imperial guard are after thieves they believe to be spies of Gartland.

Otaru, Lime, and Hanagata take a tour of the shogun's museum in the Japoness castle. When Lime accidentally breaks a national treasure, the trio are chased throughout the castle. The antics are interrupted when Panther, one of Faust's saberdolls, suddenly appears to assassinate the shogun!

Cherry loves Otaru deeply, but Lime constantly gets in the way of her affection. Determined to get him alone, she arranges for some local thugs to abduct her and send a random note. However, once Otaru arrives at the warehouse things don't go as planned.

Shogun Ieyasu explains to Otaru, Lime, and Cherry why the two marionettes are different from others: the contain a special maiden circuit that gives them emotions. Before he can explain Otaru's role, however, Faust himself appears flanked by his saberdolls to threaten the shogun.

Like Lime and Cherry, Bloodberry is completely enamoured with Otaru, but espite her advances and marriage proposal, he is uninterested. When a dazed and confused Otaru mumbles he wishes he could fly away, Bloodberry takes it upon herself to make this dream come true. Unfortunately, they crash on Mt. Kamuna where the terrible beast Ponta lives.

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 goes up in smoke, their only remaining hope is the mysterious lottery ticket.

While Otaru and the marionettes are working at a haunted house, thieving marionette collectors out to steal Cherry wind up taking Lime instead. Hanagata, wishing to declare his own love for Otaru, tries to talk him out of going to rescue her. A confused Otaru is faced with society's views on marionettes and his own growing love for Lime and the others.

Faust succeeds in defeating Petersburg, one of the six cities on Terra II, and his sights are set on Japoness. Otaru, carried away by thoughts of being a hero, agrees to the shogun's request to sneak into Gartland to destroy their main computer. Fearing that war will make her lose Otaru, Lime foolishly sets off by herself.

Otaru, his marionettes, and Hanagata have finally arrived in Gartland and are dismayed by the sight of ruined buildings and people starving in an oppressive police state. Their attempts to break into a food bank to help alert the city's guards to their location and provide a useful distraction while Cherry and Otaru plant bombs on the main computer.

Surrounded by the saberdolls, Otaru and the others look defeated when the child they met earlier leads them to a secret hiding place. Gartlant's citizens are just as eager to defeat Faust as they are and help them prepare for a second attempt on destroying the main computer. It won't be easy, though, because this time Tiger and the saberdolls will be expecting them.

Although it allowed their mission to succeed, Otaru's marionettes are upset and sulking after he kissed Luchs. They come upon an abandoned hot springs resort and see it as a way of lightning everyone's spirits on the trip home. Everything is going well until a plasma storm starts brewing underground.

After saving it from Gartland, Japoness gives everyone a hero's welcome. Otaru gets swept up in his newfound celebrity status and begins to live a life of fame and fortune, all while his marionettes go ignored. Lime, Cherry, and Bloodberry do not want to ruin his happiness and feel he is better off without them.

In order to finally decide which of them most deserves Otaru, Lime, Cherry, and Bloodberry enter a contest to decide the best marionette on Terra II. In spite of their paper-thin disguises, Tiger, Luchs, and Panther successfuly join the contest as well in order to lure Otaru over to Gartland's side.

Shogun Ieyasu summons Otaru, Lime, Cherry, and Bloodberry to the pioneer museum where Lime first awakened. There he explains how the maiden circuits work, allowing them to grow and develop like normal people. The maiden circuits will play an integral role in reviving the human female. Before he can go into further detail, however, agents from Gartland set the museum ablaze.

Lime adopts a squirrel as a pet, but Otaru warns it is a big responsibility. When it gets sick, Lime and the others come to terms with the heavy concepts of life and death, and that living things can not simply be repaired like marionettes.

Faust gives the saberdolls one last chance to wreak havoc on Japoness before casting them out forever. They slip in to kill the shogun while a huge, black machine distracts everyone. Suddenly, as the machine is poised over the city, Cherry recognizes that it's a huge bomb.

A gigantic bomb hangs over Japoness and the saberdolls are at the borders. Otaru springs into action but Lime, devastated by Shogun Ieyasu's death, refuses to leave his side. Even with Cherry and Bloodberry, the battle is turning one-sided and a plasma storm rages overhead.

With the shogun dead, and no living heir, Bloodberry muses on who will run Japoness now. The shogun and his chamberlain, whose minds were uploaded to Tamasaburo and Baikou, continue to advise the Japoness parliament during the restoration. Meanwhile, the saberdolls are given an ultimatum: bring Faust the maiden circuits or die trying.

When a distraught Lime flees in horror at Tiger's death, she is found by Souemon Obiichi who tells her he knows of a way to be rid of the heartache. Otaru and others discover Lime laying there, her maiden circuit removed. Everyone agrees to help comb Japoness, including Obiichi who tells a grief-stricken Otaru that Lime is still Lime and he should remain with her.

In order to celebrate Lime's recovery, everyone in the Kasahari Apartments are going to have a big barbecue. Having forgotten to bring plates, old man Gennai sends Otaru to a nearby pottery forge that a friend runs. Although unintentional, Otaru's refusal to bring Lime and his seemingly distant attitude causes her to become depressed. Back in Gartland, a new invention allows the sun to shine through for the first time.

Faust's latest creation, the chimera-like Saber Beast Leopard, is dispatched to take the maiden circuits once and for all. Otaru and the others are summoned to a meeting with Terra II's leaders in order to discuss a matter of grave importance.

The Earth colony ship, the Mesopotamia, was designed by Lorelei to be a thinking and feeling machine. Before she could perfect the ship's emotions, it too fell in love with her, condemning the Humans to death. For ten generations Faust has plotted to save her, no matter the cost. Now that Lime, Cherry, and Bloodberry's maiden circuits have fully matured, the Mesopotamia has awoken and begun a relentless attack on the planet below.

Faust and Ieyasu explain to Otaru that the only way to stop the Mesopotamia is for the three maiden circuits to act as a replacement for Lorelei. However, the only way of reaching it is by combining the Japonessgar and Gartland's Sabbelburg 2. Not wanting to lose the marionettes, Otaru instead opts to head there by himself to destroy the ship and save Lorelei.

As the Marionettes, aboard JaponesGar, approach the Mesopotamia and missiles begin to explode all around them, Luche feels the Mesopotamia's feelings - love for Lorelei, anger at those that would take her away - resonating in her otome kairo and Lime hears Lorelei's voice again, telling her to flee while she can. But then, the computer's chattering mind suddenly stops, and as the attack on the surface of Terratoo continues, JaponesGar punches through the Mesopotamia's hull. Once inside, it doesn't take Luche long to ascertain the location of the heart of the Mesopotamia's computer. Though the Mesopotamia's interior defenses are more than adequate, they're no match for the Marionettes and Saberdolls. In fact, one of the rockets launched at the Marionettes is quickly put to a most unintended use, as the girls turn it around and ride it down the dark corridor, laughing all the way.

Otaru's in charge of the Sanja festival, and it looks to be a big success. Lime, Cherry, and Bloodberry become very interested in the float race when they discover that the winner has one wish granted. Of course, they all want the same thing, to be alone with Otaru.

Otaru and the Marionettes fight against the evil Faust, whom is about to take off on the Japonessger with Lorelei. However, a surprise ally appears and disrupts Faust's plans.