The heroes are on a train to Lake Acuity, where Ash will battle Paul. He raises his voice that he scares a man and they get his sandwiches. The nervous man thanks them for getting the lunch and tells them to keep them. The gang introduces themselves, while the man is Looker. Looker gives more sandwiches to the strangers (which are Team Rocket) and goes to give the other sandwiches to other staff of the train. Brok heard there is a Pokémon powering the train, so they go to see which one it is.
Ampharos uses Thunderbolt, powering up the train so that it goes faster. The heroes see the Ampharos and the conductor tells them Ampharos is invaluable to the train. Looker gives them sandwiches, but the train stops as they see a red light. Team Rocket plans to get Pikachu sometime later and also feel they stopped. The driver reports to the station and has heard there is no malfunction, but neither is there an order. The conductor thinks there is trouble ahead and goes to witness, though Looker wants to come with him. The driver goes to report to the passengers what happened, while the heroes go to get lunch.
As the heroes have lunch, Team Rocket is disgusted to see them happy and go to get Pikachu. The conductor apologises for trouble, but advises them to go outdoors. Jessie gets angry, so Meowth and James calm her down and heed his advice. Looker sees the tracks are new and not rusted, while the river has seen the controls changed. Looker knows someone wanted to use the unused track. The driver goes to report to the station, while Looker investigates. The heroes had lunch, so Ash's Pokémongo to train against Paul. However, Team Rocket takes (almost) all the Pokémon with them. The driver demands the Pokémon returned, but Team Rocket goes up. Ampharos uses Signal Beam, which causes the Pokémon to escape.
A net is released and Happiny, Piplup and Pikachu are captured. Ampharos goes on the net, which is swung. Ampharos uses Signal Beam to destroy the remote control, but hits the balloon, causing it, Happiny, Pikachu, Piplup and Team Rocket to be sent away. The heroes go to save them, even if the conductor tells them not to. Looker has found a strange building where the tracks end. Ampharos' ThunderPunch cuts the net, releasing the Pokémon. Team Rocket is angry for this act, but the balloon falls, so the Pokémon run away. Staraptor has not found anything, so Dawn sends Buneary and Brock his Sudowoodo to search.
The Pokémon have come to a crossroad. Piplup and Happiny take a direction, but soon run back, as Fearow attack. Ampharos and Pikachu attack, however they miss and retreat. Seeing no other option, the Pokémon jump and the Fearow go into other direction. The driver gets a call from the conductor and hears Team Rocket stole the Pokémon. The Pokémon face a giant boulder and it cannot be pushed easily. Ampharos uses ThunderPunch, but nothing is made. Piplup uses BubbleBeam, but he also does nothing. He tries with Whirlpool, but the result is same. Happiny comes and lifts the boulder with ease and tosses it in a river. Looker sees the tracks go to Lake Acuity. He uses some googles to see that someone was here and gets an object amidst the rubble.
Buneary has spotted something and the heroes follow her. Staraptor confirms this as well. Piplup gets exhausted and soon, the Pokémon fall in a hole. Team Rocket caught them and get them in a sack. However, Staraptor's Aerial Ace gets them loose. Jessie sends Seviper and James Carnivine. Seviper uses Poison Tail and Carnivine Vine Whip. Sudowoodo charges, evading Vine Whip and hitting them with a new move, Hammer Arm. Pikachu uses Volt Tackle, blasting them off. The drier came back, as well as the heroes and Looker. The light turned to green, so they all continue as Ampharos powers the train via Thunderbolt. Ash cannot wait to have the battle, and Looker passes by, telling them to enjoy the youth as best as they can. Looker goes out, reporting Team Galactic used the train system to transport something to Lake Acuity.
- Professor Oak's Pokémon lecture takes a ten episode hiatus beginning with this episode.
- Jessie's Yanmega was the only one of the main characters' Pokémon not to appear in this episode.
- Darkrai returns, replacing Regigigas in the first part of the preview of the next episode.
- Ash and Brock no longer wear their jackets as of this episode, and Dawn has returned to her normal clothes.
- The dub title comes from the saying "Frozen in their tracks".
- Music from Pokémon Heroes is used as background music.
- During the picnic scene in the English dub, Croagunk's Japanese voice can be heard.
- When Looker gives the packed lunches to the conductor, Ash's hair and fringe are missing.
- On Pokemon.com, the episode's title is "Frozen on the tracks", instead of "Frozen on their tracks".