When Molly Holmes moves with her family to Horseshoe Bay, her grandmother gives her an enchanted shell necklace that magically transforms her life. The power of the necklace transports Molly to the Undersea Kingdom, where she discovers that she is a secret mermaid and meets lots of new mermaid friends.

As Molly's underwater quests begin, she must help fellow mermaid Ella recover her piece of the magical conch shell in order to protect the coastline and prevent floods. But the Dark Queen's army of menacing sea creatures is hot on the mermaids' tails.

Secret mermaid Molly must help her mermaid friend Delphi to find the second piece of the enchanted conch shell in time to prevent a terrible oil spill.

Swimming with the turtles and tropical fish in the ocean reefs has always been such fun for the mermaids, until the reefs begin to die. Molly must help her friend Coral find her magic shell so she can rescue the reef - but the wicked Dark Queen and her army have other plans.

Mermaid Molly sets off with Coral, protector of the ocean reefs, to find the third piece of the enchanted conch shell. With it, they would be able to restore the dying tropical reefs and return a host of sea creatures, including a lost baby turtle, to their rightful homes. But first they have to beat a swarm of the Dark Queen's evil jellyfish.

In the climax to the mermaids' search for their pieces of the magical conch shell, Molly finds herself in the frozen seas of the Arctic. There she discovers that the Dark Queen has stolen the last conch piece and imprisoned ice mermaid Shivana.

Molly is called back by the Mermaid Queen because the mermaids desperately need her help. All the whales, turtles, seahorses, octopuses and dolphins have vanished from the seas and the mermaids expect dark magic is at work. Molly believes the answer to their whereabouts might lie in a strange sparkly ball she spotted in a rock pool.

Many sea creatures have suddenly gone missing and Molly is determined to help her friends find them all. The seals have reported hearing strange, distant dolphin noises, so Molly and Aisha go to investigate. When they discover a magical shell with the thousands of tiny dolphins trapped inside, they have no idea how to release them.

Continuing her quest to rescue the sea creatures who have been spirited away by dark magic, secret mermaid Molly helps her friend, Animal-Keeper mermaid Phoebe, to track down the lost penguins. A clue from some friendly seals leads the mermaids into icy water, where it seems the penguins are trapped at the top of a huge iceberg.

When Molly is plunged back into the magical Undersea Kingdom, she finds the Merqueen waiting with bad news - the Dark Queen Carlotta is back, and it is she who has been hiding sea creatures away and stealing their powers. Now it's a race against time to track down the animals that are still lost.

All of the creatures missing from the magical Underwater Kingdom have been found now, except for the octopuses. When Molly and Animal-Keeper mermaid Iona track them down they are surprised to find that there are no monsters on guard. Then a basking shark brings the message that the mermaid palace is under attack from the Dark Queen.