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 Pokémon 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 Pokémon. But Team Rocket was also on the train, and they drop by in their Meowth balloon to steal all the Pokémon. The engineer orders Ampharos to stop them, so Team Rocket settles for stealing Pikachu, Happiny, and Piplup—except Ampharos comes along for the ride and crashes their balloon! As Ampharos and the three Pokémon escape into the forest and begin their long, dangerous walk back, Looker slips away from the conductor and turns to be quite the super-sleuth. He has a good idea of who stopped the train, and he’s looking for clues!
Ash’s Staraptor spots the lost Pokémon, 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 Brock’s 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!
Having left Snowpoint City behind, Ash and his friends are now aboard a train leading to Lake Acuity, where Ash is due to have his Full Battle against Paul. There, Ash and the others meet an absentminded man named Looker, who is also on the train, and is almost knocked over when Ash shouts his determination to win. He drops the lunchboxes he is carrying, which Brock, Ash, and Dawn are all able to catch. Ash apologizes and asks Looker if he is okay, and he says he is. Brock asks him if the boxed lunch was the train station's best food, and Looker gives Ash, Dawn, and Brock one as a gift, saying that he had accidentally ordered too many from the seller. The gang introduces themselves to Looker, and Looker introduces himself. Team Rocket, in disguise, also receive the boxed lunch from Looker. Looker also decides to give boxed lunches to the driver, his assistant, and the driver's Pokémon.
As the train travels on to Lake Acuity, the driver tells his Pokémon, an Ampharos, to use Thunderbolt. The driver's assistant tells the gang that the train is powered by Ampharos's Electric attacks, impressing the group with the cooperation between Ampharos and the driver. Looker gives the boxed lunch to the train crew when the driver suddenly stops the train, as the signal ahead is set at red for danger.
The driver decides to check what is happening. However, when he makes a call, he is informed that there is nothing wrong with the line ahead despite the signal that says otherwise. As there may be a problem with the line that hasn't been relayed to the operators, the assistant and Looker decide to go outside and check while the driver goes to inform the passengers of the situation. Meanwhile, the gang decides this is the perfect time to eat their lunches, and as the train is delayed, they decide to eat it outside and let their Pokémon out of their Poké Balls for a while. Team Rocket decides to take advantage of the opportunity and make an attempt to steal all of the Pokémon. As they are about to leave their seats, the driver tells them not to worry, and they can watch the scenery. In a bad mood, Jessie almost tells the driver about their intentions, but Meowth covers her mouth in time.
Outside, Looker discovers that the track, which supposedly hasn't been used for a long time, doesn't have one speck of dust on it, implying it is being used on a regular basis now. The assistant replies that it could be a prank, but the junction points on the disused line have also been changed. Looker realizes that the points were changed intentionally, and the assistant tells Looker to go back to the train while he investigates further. However, rather than head back, Looker heads down the mysterious line.
Ash decides it is the perfect time for him and his Pokémon to get some quick training done before the battle against Paul. Then, a strong wind suddenly appears. However, it is not a wind, but Team Rocket with a new suction machine attached to their balloon that sucks up everyone's Pokémon, besides Grotle and Mamoswine. The gang demands their Pokémon back, but Jessie refuses. Team Rocket prepares to make their getaway when the driver notices what is happening and has Ampharos use Signal Beam on the balloon. This allows most of the Pokémon to escape, but Pikachu, Piplup, and Happiny get caught in a net. Ampharos jumps up to the net while the driver commands it to destroy the remote control. However, it doesn't work, and Ampharos only creates a hole in the balloon, sending them all flying away together with Team Rocket.
At the end of the disused line, Looker finds a warehouse and heads inside. Meanwhile, Ampharos is able to use Thunder Punch on the net, freeing the three Pokémon while Team Rocket and the balloon fall to the ground, knocking them out. Ash has Staraptor look for the missing Pokémon, while Pikachu and the others arrive at a junction. They immediately encounter an angry flock of Fearow, which pursues them. Soon, all four come to a cliff and have no choice but to jump in order to escape. Meanwhile, the assistant receives a call from the driver, learning that the Pokémon had been stolen by Team Rocket.
Continuing the search for their Trainers, the Pokémon find a big boulder blocking the way. Pikachu and Ampharos are unable move to it. Piplup tries to use his Bubble Beam and Whirlpool to move the boulder, without any success. Happiny ultimately uses her strength to move it. Meanwhile, inside the warehouse, Looker realizes the disused track leads directly to Lake Acuity. Taking out his goggles, he finds footprints on the floor and a piece of paper.
Pikachu and the others continue their journey, but are caught again by Team Rocket. Luckily, Ash and the others arrive, and Staraptor frees the Pokémon with Aerial Ace. Team Rocket sends out Carnivine and Seviper in retaliation. During the resulting battle, Sudowoodo uses a new attack, Hammer Arm. Then, Pikachu finishes Team Rocket off with Volt Tackle, sending them blasting off.
At sunset, the assistant, Looker, and the gang return to the train. Looker claims to everyone that he took the time to look at the scenery. With the signal and junction set correctly, Ampharos is ready to move the train again to Lake Acuity. Looker wishes Ash good luck for his battle against Paul, and Ash thanks him. Later, at the back of the train's carriage, Looker calls his superiors and explains that the organization that stopped the train is moving something to Lake Acuity, adding that he will continue his investigation. He then takes out and looks at the piece of paper that he found in the warehouse, which carries Team Galactic's logo.