The country of Moiria is having it's Gym Challenge, but this year there's a change. The gyms will be faced by teams of trainers and their pokemon, and the challenges will be less straightforward than "fight against some idiot with a monotype team." To show off this new style of fighting, an exhibition match is held in Port Amethyst. There, a team of five trainers were randomly selected to fight with each other. They are:

They beat their opponents in the exhibition match, but on the way out they run into a mysterious woman wearing a uniform with a red R on it. She invites them to join Team Rocket, but when they turn her down she decides to steal their pokemon instead. However, it turns out they fight just as well together in unofficial battles and the woman is forced to flee. The police show up soon after, take their statements, and send them to the hospital so their wounds can be seen to. Afterwards, they decide to form a team, both to take on the gyms and in case Team Rocket decides to take retribution.

After spending a day training (meeting a photographer from a foreign land along the way), they take on the first gym leader and defeat him. He gives them tips on where to go to get money and passage to another island. Following the first piece of advice, they go to the local industrial park to scavenge. However, while there they happen to run into another Team Rocket operation led by a man in a suit. The man warns them to leave, but the party decides to fight them. The police are called, but don't arrive until the rockets are captured.

The next day, the team leaves Port Amethyst to set out for Sandy Shore, and the second gym. Aboard the boat they meet Captain Lennox, an old sailor with a missing leg. He tells them the story of how he lost it in a fight with a giant Sharpedo. They make it more or less safely to the next island, where they meet a young woman interested in joining their team

They go to the museum where the gym is supposed to be located and decide to take a tour. They see a lot of old stuff, including a replica of one of the orbs that figured in a recent incident involving time travel. They also learn the gym leader, Professor Acacia,  is away on a dig, so they set off to find her. However, when they arrive at the dig site and prepare to battle, there is an explosion and Team Rocket appears, this time led by a thug with green hair. The professor is grabbed and taken away and another fight breaks out. The team defeats the Rockets, but an explosion collapses the ruins.

They return to Sandy Shore (with a prisoner in tow) to discover the museum has been broken into. After getting nowhere with the police, the party decides to take matters into their own hands and set out in search for the missing professor themselves. After determining the most likely place to look was the professor's last dig site, they take a ship straight to it. Inside the ruins is a rocket base, where they capture a number of scientists and discover the rest of the Rockets are just about to leave.

The team heads downstairs where they find a man with glasses waiting for them. He challenges them to a duel for the professor, which the party wins. Before leaving, the man explains that he was waiting for the police, tells the party to pass on the message that Team Rocket "would very much appreciate it if the Kyogre Orb was delivered to us," and leaves with the rest of Team Rocket on their submarine.

Upon return to Sandy Shore, the professor awards the party their second badges. She also explains that Team Rocket had kidnapped her because they wanted to know about the the Rune Gates. However, she knew neither their purpose nor how to activate them.

The team decides to ignore all that and continue the gym challenge, heading to Ebony City. There they run into Cyrus's ex-girlfriend, and his past as the son of a cult leader comes to light. However, they decide to ignore that to and continue with the gym challenge. But before they can, Captain Lennox says he found the location of the Sharpedo that took his leg and invites them to go hunt it with him. They agree, but during the fight Vessin is knocked unconscious and falls in the water. A search reveals that he may have been washed into one of the Twisted Gates.

They start a manhunt for him, eventually stumbling across a Bed and Breakfast located by one of the gates. There they learn old myths surrounding the gates; that they were used to contact legendary pokemon after making blood sacrifices and that sort of thing to activate them. This gives them an idea, and they return to Sandy Shore. There Cyrus has his pokemon attack him, making himself a blood sacrifice for the gate. It takes him, but he's able to find Vessin and teleport back out with his mystic powers. Meanwhile, Islief's status as a Ranger is finally revealed and Rhiannon takes to Jade in private.

The next day they telport back to Ebony City and finally take one the gym! Also they find out the professor used to work with both Brun and Cyrus's father. They both win and are granted tickets to take the train! They decide to go to Ivoryville, but on the way they find...

She's being attacked by Team Rocket and asks for help, so the party interferes. During the fight, a woman with white hair joins the fray and appears to become possessed. The cars the party are in derail from the train and start tumbling down the hill. The fight continues and the woman is forced to flee. The party are then picked up by EMTs and taken to Ivory Town.

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