Team Plasma’s quest to awaken and control Reshiram continues, while our shackled heroes watch helplessly. Axew sneaks out of Iris’s hair, where it’s been safely concealed, and manages to free Iris and Cilan from the metal bands that hold them. Then, Concordia and Anthea appear from their mysterious fog and ask N to come back into hiding with them. But N vows to stay in the “real” world and fight for his ideals. Dr. Colress’s device has taken control of their Gothitelle and Gardevoir, along with the newly awakened Reshiram, and things are looking very bleak indeed.
Now is the moment for Team Rocket to step in! They’ve been watching the goings-on from a safe distance, but when Looker spots them and asks for their help in destroying the device and freeing all the controlled Pokémon, they agree. Meowth jumps in to distract the other members of Team Plasma while Ash and Pikachu go after the device. Colress tries desperately to take control of Pikachu, but Pikachu’s willpower—and its bond with Ash—proves too strong, and Pikachu aims a Thunderbolt at Reshiram to break it free as well. The device is destroyed, and Team Plasma is defeated, thanks to an unusual bit of teamwork between our heroes and Team Rocket!
Reshiram is free, but it’s still very angry. N speaks to it in an attempt to calm it down, and it soon becomes clear that he’s changed his tune when he tells Reshiram that people and Pokémon can live in harmony and work together. He promises Reshiram that he’ll keep fighting for an ideal world for everyone, people and Pokémon alike, and seems pleased with Reshiram’s answer. Iris wants to know what the Legendary Pokémon told him, but Ash disagrees—he wants to meet Reshiram again someday and hear its answer for himself!
The story begins immediately after the events of the previous episode, with Ghetsis performing a ritual to awaken Reshiram. As the Light Stone begins to float, Ash prepares to intervene, only for a mysterious fog to fill the White Ruins. The Team Plasma Grunts holding N are suddenly scattered by a Psybeam, followed by a Magical Leaf that destroys N's bonds. From the heart of the fog, Anthea and Concordia call out to N, asking him to return with them.
While Axew tries to release Iris, N explains that Team Plasma is trying to awake Reshiram, which he fears will repeat the tragedy he saw years ago. Anthea and Concordia again ask him to return, saying that he is too important to lose, but N refuses - he has to find out why Reshiram is so angry, or humans and Pokémon will never be able to understand each other. He begs Anthea and Concordia to help him defeat Team Plasma, prompting Anthea and Concordia's Gardevoir and Gothitelle to appear from the fog. However, Colress uses his Pokémon Control Device on the Psychic Pokémon, bringing them under Team Plasma's control.
As the brainwashed Pokémon subdue Anthea and Concordia, Reshiram finally awakens from the Light Stone, causing everyone to stare at it in awe. Axew releases Iris and begins working on Cilan's bonds as N tries to speak to Reshiram, only to find that the dragon is still filled with rage over its previous awakening. Welcoming Reshiram back to their world, Ghetsis declares that the Vast White Pokémon will obey him, with Colress using his machine to take control of Reshiram. At Ghetsis's command, Reshiram attacks with Fusion Flare, scattering friend and foe alike. Cedric Juniper and Ash's friends run for cover as Team Plasma's brainwashed Pokémon are blown away by the force of Reshiram's attack, while Ghetsis berates his minions for their incompetence.
Ecstatic at the success of his experiment, Colress commands Reshiram to launch another Fusion Flare, declaring that its true power is yet to be revealed. As Cilan sends out his Crustle to free Cedric Juniper, Ash resolves to find a way to save the Pokémon from Team Plasma's control. Watching from above, Team Rocket prepares to steal Colress's machine, both to further their own plans and to derail Team Plasma's. However, Looker finds them and asks them to help him destroy the machine. After a moment's thought, Team Rocket agrees to help, declaring that this will be their "time to shine".
Colress aims the control ray at Ash's Pikachu, but Ash stands in his way, vowing to protect his Pokémon. Colress simply readjusts his aim, only for Meowth to drop in and use Fury Swipes on some of Team Plasma's Pokémon. Leading Ash and Pikachu behind some cover, Meowth explains that Team Rocket is helping Looker to destroy Colress's device. Ash asks Pikachu to stay hidden while he distracts Colress, but Pikachu rushes to his aid when Aldith sends the brainwashed Pokémon to stop him. Seeing that Pikachu is coming to help, Ash orders a Quick Attack preventing Colress from locking on to the Mouse Pokémon. While Iris, Axew, and Team Rocket battle the brainwashed Pokémon, Ash and Pikachu make a break for the machine, forcing Ghetsis to send Reshiram to stop them.
With the Legendary Dragon blocking their way, Ash tells Pikachu to use Electro Ball on Colress's machine. However, Colress uses the opportunity to blast Pikachu with a mind-control beam, interrupting its attack. To everyone's surprise, Pikachu appears to be resisting the effects of the machine, prompting Ash and his friends to offer words of encouragement. Colress gloats that Pikachu's struggles are futile, but his confidence turns to astonishment as it manages to turn around and begin advancing on the scientist. As Colress stares in bewilderment, Pikachu releases a powerful Thunderbolt at Reshiram - suddenly, N declares that he can hear Reshiram's voice as well. Cilan realizes that Reshiram is using Pikachu's electricity to try to escape from Team Plasma's control.
Frustrated and confused by this turn of events, Ghetsis commands Colress to secure their control over Pikachu. In response, Colress blasts Pikachu with his machine's full power, but this only stalls the Mouse Pokémon for a moment before it continues advancing on Team Plasma, even firing another Thunderbolt that comes dangerously close to the device. As Colress and Ghetsis look on, stunned at Pikachu's resistance to their control, Ash commands Pikachu to launch an Electro Ball at Colress's machine. Reshiram adds a Fusion Flare to the assault, which Colress narrowly evades as his machine is finally destroyed. With the device in ruins, all of the brainwashed Pokémon return to normal. A distraught Colress wonders what went wrong, to which N explains that he underestimated the power of the bond between Ash and Pikachu. Colress insists that he won't give up, only to be interrupted by an enraged Reshiram igniting its tail. Stunned and disbelieving, Colress declares that Reshiram's power is rising even higher than when it was under his control, emphasized by the Legendary Dragon using Blue Flare to destroy Team Plasma's jet.
Before Reshiram can continue its rampage, N begs it to stop. Having observed the strong bonds between Ash and his Pokémon, N tells Reshiram that his ideal world - a world where humans and Pokémon can learn to accept each other - can exist alongside Reshiram's world of truth. This serves to calm the Vast White Pokémon down, even as an infuriated Ghetsis rages at it. As Aldith and Barret attempt to convince their leader to flee, Ash and his friends spring into action, using their Pokémon to imprison the villains in a ring of rock and ice.
With Team Plasma contained, Reshiram prepares to leave, but N halts it with one last question: how does it feel after seeing humans and Pokémon come together against evil? After a moment, N smiles at Reshiram's unheard answer and bids it farewell, telling it that they will meet again someday. As Reshiram flies away, Iris asks N what Reshiram told him, but Ash says that it doesn't matter - they'll find out the answer when they next meet Reshiram, giving them something to look forward to.
The International Police arrives to arrest Colress, Ghetsis, and the Team Plasma Grunts. Despite their failure, Colress has regained his spirits with the thought of a new project: a machine to allow humans to understand Pokémon. Meanwhile, Ash, Iris, and Cilan part ways with N, who convinces Anthea and Concordia to travel with him on their quest to create their ideal world, one where humans and Pokémon can truly understand each other.