Like many popular mahou shoujo series, the Pichi Pichi Pitch manga is divided into distinct story-arcs, comparable to parallel seasons of the Pichi Pichi Pitch anime. However, the story arcs of the manga have yet to be titled with any official names, so for the time being, I'll simply refer to them as "first story arc," "second story arc," etc.
The First Story Arc
The first story arc of the manga consists of the first twenty chapters, or volumes 1-4 in their entirety. The mermaid Lucia assumes a human form and travels to dry land in order to find her long-lost pearl; when she finally does find her pearl, she also finds Kaito, the boy that she loves. Now Human Lucia has to win Kaito's heart, without revealing her mermaid identity to him. This in and of itself would be difficult enough, but even worse, Kaito is already in love with her mermaid self!
But Lucia has another burden to shoulder as well. She and her new friend Hanon are two of the seven mermaid princesses of the seven ocean kingdoms. Together, they must search for the other remaining mermaid princesses, and combine the power of their seven pearls to summon the ocean goddess, Aqua Regina. Aqua Regina is apparently the only being powerful enough to stop Gakuto, a mysterious villain who is terrorizing the ocean world. The problem is, many of the ocean kingdoms have already been destroyed by Gakuto, and the mermaid princesses have scattered, either gone into hiding, or already entrapped within Gakuto's castle.
Basically, the first story arc of the manga is about Lucia and Kaito's romance, set against the backdrop of the story of Gakuto and the Dark Lovers. If you want more spoilers, go read the manga yourself!
The Second Story Arc
The second story arc of the manga corresponds to the second anime series, Pichi Pichi Pitch Pure. It began in chapter 21 and continues through chapter 30, comprising volumes 5-6 of the manga.
It looks as though peace has returned to the ocean. Lucia and Kaito are finally able to consummate their love, but on their first night together, Kaito breaks some sad news. He's going back to Hawaii, to compete in a surfing tournament. But don't worry! He'll only be gone for one week. Lucia and Kaito reassure themselves that there's nothing to worry about.
But Lucia *is* worried. She has strange dreams in which a child's voice calls out to her, asking for help. She has visions of a mermaid kingdom in ruins, and of spheres of light filling the ocean... And then disaster strikes. A ship that Kaito is traveling on is involved in an accident, and Kaito is lost at sea.
Refusing to believe that Kaito is dead, Lucia plunges into the ocean, searching for him. Her search leads her to the ruins of the Indian Ocean Kingdom, where she sees a ghostly vision of Sara. Sara explains that her kingdom is preparing for the birth of a new princess, Seira. The spheres of light that Lucia sees filling the ocean are made of the life force of the Indian Ocean. The spheres are gathering inside the Orange Pearl, becoming pieces of what will eventually be Seira's heart. But, in Sara's words, "a terrible malice" is haunting Seira. And then the force of this mysterious evil appears: He is Michel, an angel who claims to represent God. Michel wishes to destroy the human world and create a new paradise where his own "wonderful species" will reign forever. When Lucia refuses to join with him, Michel attacks, stealing the fragments of Seira's heart, and absorbing them into himself.
Now Lucia has a new mission. She must take back the fragments of Seira's heart, even if it means fighting for them one fragment at a time.
However, Lucia is quickly buoyed by wonderful news. Kaito is alive, and he's returned to Japan! But when Lucia meets Kaito at school, she is shocked to discover that during his accident he was struck on his head... and now he doesn't remember ever having met her before. But could a mundane blow to the head really be the reason that Kaito suffers from such unusual (and selective) amnesia? To make matters even worse, Kaito was apparently saved, and is now being cared for, by a kind, gentle girl named Michal. Kaito has brought so much happiness to Michal's lonely, isolated life. And Michal isn't about to give him up to some girl that he can't even remember!
The Third Story Arc
This story arc consists of three special short stories. "Hoshi Furu Umi no Serenade" ("Falling Stars Marine Serenade") deals with the unfinished subplot of Yuuri and Hippo's tragic romance. "Tsubasa no Message" ("Winged Message") is a brief episode from the lives of Rihito and the reborn Michal. Finally, "Soshite Mirai e Super Love Song!" ("And then, A Super Love Song to our Future!") is the final, ultimate ending of the manga - and a glimpse into Kaito and Lucia's future. To say any more here would be to spoil the lovely surprises that you'll discover when you read these stories yourself!