On the way to Mossdeep City, Ash and friends encounter Spoink again. It is floating on a log and a wave knocks it off. They rescue it, but it starts jumping around and the pearl on its head falls into the ocean. After searching the ocean with Mudkip and Corphish, Ash and friends head for a nearby island with the sad Spoink. There, they meet Isiah who is studying a blue pearl. Team Rocket tries to steal it, but Spoink ends up foiling their plans and runs off with the pearl!

On their way to Mossdeep, Ash and Co. stop on a beach and they see a diver coming on the beach with a box.The man goes up to them and show them a necklace made of Green Shards.He said he found it on a Relicanth so he brings them to his shop and say he's going to looks for the treasure of a sunken ship.Ash and Co. agree to go with him and they go in a sub. Meanwhile in their Magikarp Sub,Team Rocket sees all the Relicanth underwater so the plan to steal all the Relicanth and the treasure so they can give it to Giovanni.

Ash and the gang are still on their way to Mossdeep when Max says that, according to the PokeNav, there are three islands approaching called the A, B, & C Islands , one of which has a Pokemon Center. However the journey is interrupted when a bunch of kids ride past on a bunch of Huntail and Gorebyss, which both evolve from Clamperl. While at the Pokemon Center, the group hear a brother and sister arguing about if Huntail or Gorebyss are better than each other, which is a rivalry between the other two islands. While attempting to mediate the quarrel, Ash and the others meet up with their old friend Professor Birch, who explains he is on the island to investigate the mystery of Clamperl's evolution...