A group of children use mechanical puppets at village festivals. But sometimes they use them for mischief. A group of warriors attack his village.
After the attack, the children return to their village in search of their mother but find it burned. They know machine people.
On their way, the brothers encounter a samurai who is holding a member of the machine people prisoner. He with hatred claims clockwork dolls are for war.
Following the attempted kidnapping of Hiwou's sister by the Machine Men, the fight between their giant Clockwork Dolls is inevitable. They also meet a member of the Wind Gang who opposes the opening of Japan.
On their way to Takayama, the brothers are accommodated in the forest house of a kind lady who lost two children and offers to stay with the two younger brothers.
The brothers have an accident with their vessel Clockwork Doll and need to fix it. A merchant leads them to a blacksmith who is a despotic and unfriendly man.
Hiwou and his brothers arrive in a town and at the inn they find two girls who are looking for their grandfather because their mother has been killed by some mysterious Clockwork Dolls.
Winter is coming on the journey of Hiwou and his brothers, now accompanied by the two princesses. But the Wind Gang with their Clockwork Dolls chase them attacking.
They finally arrive in Takayama, the city famous for its Clockwork puppet artisans. But there is not his father who apparently has fled to make Clockwork Dolls of steam.
Foreigners cannot enter the interior of Japan but an English botanist does. The Wind Gang discovers him and wants to kill him. Hiwou protects him.
The brothers are joined by a group of samurai who are chased by the Wind Gang. They take refuge in a temple where a priest lives who is afraid of clockwork dolls. But in the fight that comes he has to overcome those fears.
Hiwou and his brothers arrive in Kyoto in search of their father, but they cannot find him. There they discover an intrigue about the lord of the place and that the two princesses are one - and a prince.
In Kyoto the conspiracy of the shogunate continues. The Wind Gang wants to make Steam Clockwork Dolls to attack Hiwou.
The New Years festival requires performances by Clockwork Dolls. The struggle of the shogunate and the emperor for the opening of the country continues.