L’école sous-marine de Namiji a fermé ses portes, et Hikari, Chisaki, Kaname et Manaka se voient contraints de se rendre à Mihama, une école à la surface. Chisaki s’enfuit après avoir subi les moqueries de ses camarades de classe. Son placenta s’assèche et elle perd connaissance. C’est alors que Tsugumu, un garçon qu’elle avait rencontré la veille, vient à sa rescousse après l’avoir trouvée inconsciente…

Alors qu'ils réalisent une poupée destinée à être offerte au peuple de la mer, Hikari réalise que Chisaki est tombée amoureuse de Tsumugu, bien que celle-ci ne le sache pas encore. Tiraillé par des sentiments contradictoires, Hikari essaie de se faire une raison. C'est alors qu'il voit Akari, sa sœur aînée, en train de sortir avec un garçon de la surface. Elle a brisé un tabou, et la punition pour cela est sévère…

Akari est blâmée pour sa relation avec un garçon de la terre. Hikari cherche à la venger, et retrouve son petit copain, mais ce dernier ne savait pas le tabou que brisait Akari. Le grand-père de Tsumugu leur apprend alors que lorsqu'un enfant naît de l'union d'habitants de la mer et de la terre, il n'a pas de placenta, ce qui explique l'exil imposé aux couples concernés. Tsumugu reserre ses liens avec le groupe, et Manaka commence à se découvrir des sentiments pour lui…

Les enfants de la mer rencontrent énormément de difficultés à s'intégrer. Chahutés par leurs condisciples, la tension monte. Hikari s'énerve pour de bon lorsque l'offrande sur laquelle ils avaient travaillé si dur est vandalisée, et il accuse à tort deux de ses camarades d'y avoir pris part. On apprend que le petit ami d'Akari était marié à une autre fille de la mer, amie de longue date de la sœur de notre héros…

Chisaki confie ses sentiments pour Hikari à Tsumugu, mais Manaka surprend la conversation… cependant, ils ne tarderont à mettre cet incident de côté : Akari décide de disparaître de la vie de Miuna et Itaru. Mais c'est Miuna qui va disparaître, et tout le monde se mettra à sa recherche. Hikari et ses amis parviendront-ils à réconcilier Miuna et Akari ? Cela est-il seulement nécessaire ?

The students get together in their swimsuits for swimming class. The sea kids are still getting used to school on land, but are starting to get along with the other kids. The teacher mentions that he's going to be timing them today and as the kids groan in response, Hikari and Tsumugu's rivalry fires up.

After school, the classmates get together in the woodshop room for the final stretch of getting the Ojoshi-sama done. After the students finish the Ojoshi-sama, even the teacher gets excited about the feat, and they wonder if it's possible to somehow do an actual Ofunehiki like they used to do with the surface and the sea working together.

Akari decides once and for all that she is going to live on the surface, and Hikari also leaves the house because he feels that Akari isn't being treated fairly.

Miuna makes a snow sea slug out of the saltflake snow that had fallen on the surface. Meanwhile, Hikari thinks about how his father is doing alone in the sea. In the sea, Uroko-sama had gathered everyone to tell them of the calamity that was about to come.

Uroko-sama tells everyone that the Sea God's powers have become much smaller than they used to be, and that the saltflake snow will continue to fall both in the sea and on the surface until the world is cold and gray.

Kaname suddenly confesses his feelings to Chisaki in front of her parents, and Chisaki doesn't know what to do. Hikari and Manaka do their best to go on with the Ofunehiki, hearing that if the Sea God gets his powers back, the disaster that is to befall their world may be stopped.

Akari makes the decision to take Ojoshi-sama's place in the Ofunehiki and head into to marriage with Itaru like she was headed toward the Sea God. That was when the preparations to try to re-enact the first Ofunehiki went back under way.

Hikari thinks of Manaka while he's at home, and decides to tell her how he really feels about her. Manaka also tries to tell him something, but then tells him that she'll tell him as soon as the Ofunehiki is over.

Five years has passed since the Ofunehiki and Shioshishio's hibernation. Without knowing how Hikari or Manaka or any of the others are doing, now a 19 year old Chisaki goes to visit Tsumugu's grandfather in the hospital.

The day of the Tomoebi, a Hikari who hasn't aged from five years ago, appears in front of Miuna and Tsumugu. He has no memory of what happened since the Ofunehiki, but seems healthy and starts living at the Shiodome household.

Hikari starts back at Hama Junior High and is in the same class as Miuna and Sayu. He fits right in instantly, making the class laugh and has his old teacher back. But Miuna and Sayu can't help but feel that the situation is weird.

Akari tells Hikari and Miuna that she was just informed that Kaname has woken up from his hibernation. They all hurry down to the Fishery Cooperative and find that just like Hikari, Kaname hasn't aged at all. Chisaki and Tsumugu also rush down to see him, but Kaname sees them together and doesn't know how to feel.

Hikari and the others find Manaka asleep within the graveyard of Ojoshisamas. They manage to bring Manaka, who is losing her Ena, safely to the surface and to the Shiodome household, but she is still asleep. Afterwards, they have a doctor examine her and are relieved to find out that other than losing her Ena, she seems to be fine.

After finding Manaka in the graveyard of Ojoshisamas, Hikari and the others bring her back up to the surface. They think that she will wake up soon just like Hikari and Kaname did, but even after a week, there is no sign of her waking up. Hikari, Kaname, and Chisaki go to Shioshishio in hopes of finding a clue to waking Manaka up.

While Hikari and Miuna are arguing, Manaka suddenly wakes up. Hikari and Miuna are obviously surprised, but Manaka acts like nothing has changed is all smiles. Other than not knowing why her Ena suddenly disappeared, she seemed perfectly fine and it's decided that she will be staying at Itaru's house as well.

Tsumugu talks about Uroko-sama and ends up with the curse fish on his arm. This makes Hikari and the others realize that Uroko-sama is not in the sea, but on land. To find out what's going on with everyone in Shioshishio, what's going to happen to the surface, and about Manaka who's lost her Ena, everyone looks for Uroko-sama.

Uroko-sama tells Hikari and Miuna that Manaka has lost the heart to fall in love with anyone. Hikari tries desperately to find a way to turn Manaka back to normal, and has a hard time facing her because of that. Hikari and Miuna decide to talk to Chisaki, Kaname, Tsumugu, and Sayu about the situation because that's how they've always solved things.

Tsumugu dives into the sea after Chisaki. He starts having trouble breathing and is about to lose consciousness, but then suddenly gains Ena. Tsumugu finally catches up to Chisaki and lets her know his feelings while they're in Shioshishio. Chisaki cries and runs away.

To stall the saltflake snow and try to get Manaka's feelings back, Hikari and the others decide to do another Ofunehiki. The day before the festival, after hearing that the red sea slug pendant has Manaka's feelings in it, Akira takes it and accidentally drops it into the sea.

In order to save Manaka, Miuna is swallowed up by the whirpool that Ojoshi-sama made and is covered in Ena that wraps around her like a cocoon. Hikari and Tsumugu go to save her but are held back by the powers of a god.