Template:Incomplete synopsis
The episode starts as Ash, Iris and Cilan look at Nimbasa City from its outskirts. Cilan then reviews its landmarks, and Ash is content to have his Gym battle. However, an exhausted Meowth insists they go to the Pokémon Center first so he can get some rest, and then tour around town. Iris then suggests this to Ash. Ash, with his Gym battle being his top priority, argues that it should be first. However, Ash soon admits he is hungry when his stomach rumbles. Cilan tells the gang to follow him to the Pokémon Center.
They then arrive at the entrance of what appears to be a subway station. Ash is confused, and thinks Cilan has made a mistake. However, Cilan, in one of his connoisseur moments, declares that this is no ordinary subway, it is the Nimbasa City Subway System! Iris, like Ash, is not hazed. Despite this, they enter the subway station anyway.
Cilan is shown to be going nuts in the station, excitedly examining a subway car on display. He explains that this is the first of the cars to be mass-produced-a system in which many things are manufactured at once, thus being produced cheaper and faster. After then IDing himeself as a "Subway Connoisseur", he ponders what that would mean. However, Meowth, irritated and impatient, drags Cilan away, much to Cilan's dismay.
Later, they arrive at the Nimbasa City Pokémon Center. Ash and Iris remark on how big it is. Nurse Joy says that's due to it being very busy. Meowth then explains of the luxourious Pokémon services, including massages. Cilan also notes that this Pokémon center is also home to a Poké Ball vault, known to contain powerful Pokémon. Meowth suggets to Ash and Iris that they have their Pokémon get these treatments, including Pikachu and Axew. They both agree, and Nurse Joy's Audino carry them there on a cart.
While they are going to the massage room, Meowth remembers something he needed to do, and delays the trip while he makes a phone call. He walks into a Telephone Booth, closes the door, and calls Dr. Zager to confirm his location. Dr. Zager then passes it on to Jessie and James.
Later, Meowth sneaks into the vault containing all of the powerful Pokemon Cilan mentioned earlier. He opens a vent and throws Pikachu and Axew, who he captured earlier, down the vent. Then, he starts throwing the Poké Balls down the vent. They all end up in Team Rocket's subway car, also known as the Ghost Train. Then, Dr. Zager makes the Driftveil Drawbridge open and the controls break. Ash goes and makes a phone call to Prof. Oak not too long after the call is made it becomes disrupted and connection is lost. Ash and his friends then tries to solve the mystery of all the strange occurrences. Nurse Joy takes the three to the vault where they discover all the Pokémon are gone. Cilan sees the air vent is open and suspects someone used it as an escape. Ash jumps down and follows the system until he reaches the end. Team Rocket takes off. They head for Anville Town, where Dr. Zager will be waiting to take the Pokémon back to Giovanni.