After bidding farewell to N and his companions, our heroes have found themselves within sight of Dragonspiral Tower. The White Ruins are close by, and Ash can’t wait to get there! But first, they must sort out a pressing problem: Pignite’s Flamethrower has gotten very weak, and after some investigation, they discover something lodged in its nose. Jumping up and down doesn’t shake it loose, and even a scary spin in the sky courtesy of Charizard isn’t enough to banish this pesky problem. Finally, Iris tries tickling Pignite’s nose with a blade of grass, and it sneezes out the culprit: a shell from Pansage's Bullet Seed attack (which had backfired onto Pignite during the earlier battle with Team Plasma)!
As they’re busy with that, Team Rocket and Team Plasma are busy double-crossing each other. Jessie and James break into Team Plasma’s lab to steal Colress’s Pokémon-controlling device, and when all the henchmen chase after them, Meowth approaches the good doctor and invites him to join Team Rocket! Colress seems intrigued, but first he wants to use Meowth in the final round of his experiments. Meowth agrees, planning to use his specially trained concentration skills to ward off the mind control...but the machine proves too powerful, and Meowth falls under Team Plasma’s influence. The machine even makes him attack Jessie and James when they return from their decoy mission! But they manage to fight through Meowth’s impressive cyclone of Fury Swipes and reconnect with their partner, and the three of them escape.
Ghetsis isn’t happy that Team Plasma hasn’t recaptured N yet, but he’s discovered something that might lead them to Reshiram—and it’s at the White Ruins. Jessie, James, and Meowth overhear this tidbit thanks to a listening device they planted at Team Plasma’s lab...so it seems our heroes, Team Plasma, and Team Rocket are all headed to the same place!
N and his companions have seemingly disappeared after transporting themselves and the group to safety. Cilan believes their encounter with N was just a dream, but Ash believes they will see N again. Axew then points out a structure in the distance, which Cilan reveals is Dragonspiral Tower, meaning they are close to their destination, the White Ruins. After a much needed stopover at a local Pokémon Center, the group head out once again towards the White Ruins.
Meanwhile, Aldith instructs the Team Plasma Grunts to capture N, while Colress is working on his Pokémon controlling machine. When Aldith is speaking with the Team Plasma Grunts she notices Jessie and James are hiding in the background. When they reveal themselves the Team Plasma Grunts use a Magnemite and Golbat to try and fight them off. Jessie and James escape from the building, with Aldith and the Grunts following them and leaving Colress in charge. Meowth reveals himself to Colress and asks him to join Team Rocket. Colress then asks permission to test Meowth in the Pokémon control machine because he is intrigued by a talking Meowth and thought he would be a great test subject.
Meanwhile, Ash, his friends, and their Pokémon finished with their lunch. Ash, Iris, and Cilan return all their Pokémon to their Poké Balls, when Ash sees that Pignite has not eaten much of its food. Pignite then uses Flamethrower on Ash, which isn't very powerful. Axew then discovers something is stuck inside of Pignite's nose, and everyone tries several ways to get it out. Ash makes Pignite jump up and down, but it doesn't work. Ash also calls out Charizard to fly into the air and spin Pignite around, but to no success. Iris then takes a blade of grass from the ground and wiggles it inside of Pignite's nose which makes him sneeze. Pignite sneezes out two of the Bullet Seeds from Pansage. The group realizes the seeds got stuck during their recent battle against Team Plasma. Meanwhile, Jessie and James are being chased by Aldith and the Team Plasma Grunts when they try and attack them once again, but fail. Jessie and James then create an energy field to trap Aldith and the Grunts in the forest and they escape. Aldith and the grunts escape by using Confusion on the wild Pokémon so they can attack the bases on the energy field, releasing them.
At the lab, Colress has locked onto Meowth with his machine and Meowth starts counting Mareep to try and stay in his own power. Jessie and James then walk in and Colress questions why Team Rocket wants to take over the Unova region, to which they reply they take what they want and have no real reason. Colress zaps Meowth with more power from his machine and Meowth soon falls under his control. Aldith and the Grunts then return and they tell Meowth that Team Rocket is the enemy. Meowth then attacks Jessie and James, so Jessie sends out Frillish and James sends out Amoonguss to retaliate. When Jessie and James are holding Meowth in their hands they count Noctowl in his ear and Meowth then comes to his senses. Jessie, James and Meowth then escape the lab thanks to Frillish's Mist.
Meanwhile, N locates another of Team Plasma's laboratories, and like the others it is completely destroyed. He spots a pair of wild Patrat and Watchog nearby, and using his abilities to understand Pokémon he learns about the successful development of the Genesect Army. N is furious that Team Plasma has meddled with Pokémon to such an extent.
While Team Rocket was unsuccessful in recruiting Colress, they were able to plant a listening device in their lab. They overhear Colress and the grunts talking to Ghetsis, who informs them the Light Stone is at the White Ruins and is the key to finding Reshiram. Team Rocket decides to head for the White Ruins too, planning on capturing Reshiram themselves.