As Meowth and our heroes arrive in Nimbasa City, Jessie and James prepare to unleash a sinister plot under the guidance of Dr. Zager. At the remarkable Nimbasa City Pokémon Center, Meowth tells Ash, Iris, and Cilan about the local specialty, a soothing Pokémon massage, and convinces them to send all of their Pokémon into the secure Pokémon Center Vault for the treatment. Meowth then makes an excuse to stay behind while our heroes head off to explore—giving him a chance to contact Dr. Zager. It turns out Meowth is still working with Team Rocket, and his apparent change of heart when he joined our heroes was nothing but a ruse!
Meanwhile, the Nimbasa Subway Bosses, Ingo and Emmet, have been investigating the mysterious “Ghost Train,” which has been spotted roaming the subway system. Now, a series of events, instigated by Dr. Zager and Team Rocket, puts Nimbasa City into chaos! But Cilan manages to put the pieces together: the Ghost Train sightings, the Poké Balls missing from the Pokémon Center, the drawbridge that leads out of town getting stuck in the open position...they’re all part of Team Rocket’s plot to pull off a huge Pokémon heist!
Cilan, Ash, and Iris take off in pursuit of the Ghost Train, thanks to Cilan’s extensive knowledge of the subway system. But numerous decoys have our heroes—and the Subway Bosses—completely flummoxed! Will they be able to rescue their Pokémon and bring Nimbasa City back from the brink of disaster?!