Team Rocket has stolen all of the Pokmon from the Nimbasa City Pokmon Center, cut off access to the city and have fled via the subway. Ash and friends give chase, and are soon joined by Ingo and Emmet, the leaders of the Battle Subway system. Will they be able to stop Team Rocket from succeeding?

Ash and friend finally arrive in Nimbasa City. Before heading to gym they decide to check out the Battle Subway. However, a mysterious event causes the Subway System to halt. They head to the Pokmon Center where strange events begin happening. Mewoth disappears and Nimbasa City is cut off from the rest of the region. Ash and friends go to help the Subway Bosses and find out what is going on.

While on the way to Nimbasa City, Ash and friends come across a Cubchoo that has been separated from its pack. They decide to help find the pack, but that proves difficult when another group of Beartic constantly attacks them.