Ash, Dawn and Brock are on a train, headed for Ash's big battle at Lake Acuity. They startle another passenger, Looker, a nervous, but kind-hearted man who tells them about the Electric-type Pokemon working on the train. Naturally, our heroes are curious to see this for themselves, so they join Looker to visit the engineer and the train's Ampharos. When the train is halted by an unexplained red signal up ahead, the conductor investigates and Looker gets off to take a walk. Looker actually suspects someone set the red signal to delay the train while they secretly used the railroad track, but who?
Ash and his friends hop off the train to enjoy a picnic lunch with their Pokemon. But Team Rocket was also on the train and they drop by in their Meowth balloon to steal all the Pokemon. The engineer orders Ampharos to stop them, so Team Rocket settles for stealing Pikachu, Piplup and Happiny--except Ampharos comes along for the ride and crashes their balloon! As Ampharos and the three Pokemon escape into the forest and begin their long, dangerous walk back, Looker slips away from the conductor and turns out to be the quite super-sleuth. He has a good idea of who stopped the train and he's looking for clues!
Staraptor spots the lost Pokemon and our heroes hurry to catch up. Pikachu, Piplup, Happiny and Ampharos stumble into a Team Rocket pit trap and are scooped up by Jessie and James, but rescue arrives just in time. Staraptor swoops in to free them as Sudowoodo uses its new Hammer Arm move to knock Team Rocket for a loop. Then Pikachu blasts Team Rocket into the skies and everyone returns to the train which is now ready to resume operation. Ash and his friends think everything is back to normal, but they don't know that Looker has identified who stopped the train in the first place: the evil Team Galactic!