Alain exits a forest and sees a Pokemon Center and proceeds to head towards it as he walks by. At that Pokemon Center, the Heroes head out to the battlefield where Clemont decides he wants to know more about Ash and Greninja and decides to do an analysis. He brings out a mini Clembot which Bonnie and Serena find cute. The "Clembot Mini", as Clemont calls it, brings up footage from the times when Greninja changed form, as Clemont put forward his hypothesis; he claims that the changes in Greninja take place only during a battle, and that they cause it to resemble Ash. He believes that the phenomenon is psychological, explaining that the mental changes cause Ash and Greninja to move and act alike. Serena claims that this belief of his is very nearly same to the prediction made by Olympia, specifically pointing that Greninja needs Ash's love to reach its new heights. Clemont adds that Sawyer did say that Pokémon and Trainer with deep bonds tend to look alike and decides that it is time to prove his hypothesis. He gives two "Battle Pulse meters", one for Ash and Greninja each, explaining that the device will collect and display changes in brain waves, heart rate and other data during a battle, as well as measure any changes Greninja experiences and how they are reflected in Ash. Ash seems pleased with the device and is excited to test it out in the battle with Clemont.
Clemont sends out his Luxray to battle and commands him to use Electric Terrain. Greninja attacks Luxray with Cut, who blocks with Thunder Fang. Luxray is asked to use Wild Charge and Greninja uses Double Team to evade the move, but Luxray manages to destroy all of the copies. Greninja appears behind Luxray and strikes it with Aerial Ace. Serena notices the display screen and notes how the waves show Ash and Greninja to be in perfect sync with each other. Meanwhile, Alain enters the Pokémon Center and is greeted by Nurse Joy and her Wigglytuff, who sees Ash though the window. Continuing their battle, Luxray uses Thunder Fang once again to meet Cut from Greninja. Clemont decides to halt the battle, as he is not seeing any noteworthy changes in Greninja; Ash claims that neither he nor Greninja know how to initiate the transformation and Clemont believes that they are missing a critical piece of information. The group is greeted by Alain; he reveals he usually meets Ash whenever he is in the middle of a battle. He notices Ash's Battle Pulse meter, and the latter explains that they are trying to find out about Greninja's mysterious power. Ash challenges Alain to a battle, and Clemont sees this as an opportunity to focus solely on the data. Alain agrees, and Clemont and Ash recall their Pokémon and give their Poké Balls to Nurse Joy for healing. Ash asks Alain what he wishes to do while they wait and asks him if he has any other Pokémon besides Charizard. Alain replies in the affirmative, and the two decide to battle until Greninja's health is restored.
Ash sends out Noivern, which upsets Pikachu who was hoping to battle against Alain. Serena and Bonnie cheer Noivern as Alain sends out his Metang. Serena checks her Pokédex, and Noivern begins by using Acrobatics; Metang counters with Metal Claw. Next, a Psyshock from Metang is intercepted by Boomburst. Ash has Noivern use Supersonic, which connects with Metang. Noivern uses Acrobatics again, but it is countered by Psyshock. Alain commands Metang to use Meteor Mash as Noivern falls, but Noivern dodges it and scores a direct hit with Boomburst. A Metal Claw from Metang and an Acrobatics from Noivern collide, but after the dust from the collision clears, Noivern is revealed to have fainted, making Alain the winner, who claims to Metang that, given more time, they would have been defeated.
Ash and Clemont's Pokémon are fully healed and as Ash puts the Battle Pulse meter on Greninja, Clemont informs a curious Alain on what his views about Greninja's transformation are. Ash and Alain begin their battle by sending out Greninja and Charizard respectively. Greninja uses Water Shuriken, but it is countered by Dragon Claw, damaging Greninja. Greninja uses Double Team to evade a Flamethrower and then hits Charizard with a Cut. Alain Mega Evolves his Charizard on the latter's advice, and then uses Thunder Punch on Greninja; the Ninja Pokémon retaliates with Aerial Ace, stopping Thunder Punch and slamming Charizard into the ground. Serena marvels at the battling Pokémon; Bonnie asks her brother if he is noticing any changes on the screen but Clemont replies in the negative. Greninja uses Cut but it is blocked by Charizard and Greninja is hit point-blank by Flamethrower; Charizard follows up with Thunder Punch to hit Greninja, who tries to retaliate with Water Shuriken. Charizard dodges though, and lands the hit, sending Greninja to the ground. Greninja starts to slowly rise upon Ash's encouragement - upon this, Clemont notes changes in the pulse waves and believes that the synchronization is about to take place. True to his prediction, Greninja changes its form and Clemont is pleased that his hypothesis is correct, proving that the Ash and Greninja's emotions must be in sync for the transformation to take place. Ash commands Greninja to use Cut but Charizard easily dodges it. Charizard uses Flamethrower which is intercepted by another Cut; an Aerial Ace is countered by a Thunder Punch. Alain is excited at Greninja's power and asks Charizard if it can feel the power too. Greninja uses Cut which is intercepted by Charizard's Dragon Claw. Charizard successfully pushes the Ninja Pokémon back and Ash feels his Pokémon's pain, though, Greninja instantly recover and hit with Cut. The attack flings Charizard back for huge damage, showering Alain in dust and dirt. Suddenly, Ash starts experiencing a mysterious pain. Serena questions on Ash's sudden behavior and Clemont notices de-synchronization of Ash and Greninja's waves. Ash finds himself unable to move and faints, while Greninja also returns to its previous form and falls on the ground, exhausted. The battle is called off as everyone rushes to aid Ash.
The scene shifts to Greninja walking away from Ash, who complains of not being able to move and pleads to his Pokémon to stop. This is, however, revealed to just be Ash's dream, with Greninja right beside him when he regains consciousness, and everyone is relieved. Alain advises Ash to rest for the entirety of the evening, and Ash apologizes to Alain for messing up the battle. Ash expresses his feelings of temporary paralysis to the group; Clemont reasons that the synchronization must have put a heavy load on him and caused him to faint. Alain is surprised at the raw power exhibited by Ash and Greninja, causing Ash to laugh off in embarrassment; Ash wonders why he wasn't able to move himself, and challenges Alain to a battle some other time, when he would have perfected the transformation. He reveals his plan of beating Alain and then the Kalos League, and hopefully be a Pokémon Master someday. Alain inquires on the Kalos League as Ash, surprised that Alain is not participating in the Kalos League, explains that only the strongest Trainers shall partake in the League, causing Alain to state that it sounds like fun.
Night sets in with Alain and Charizard sitting by a campfire, and he replies to a call from a Team Flare Grunt. The grunt shows him a video he just received from Lysandre, which is actually a message from Mairin. She informs Alain on the current state of Chespie, excitedly stating that her Pokémon has shown tiny signs of movement, and then wishes him luck as the video and the call end respectively. Alain reminisces about his time with Professor Sycamore and urges Charizard to be strong with him, so that they can protect the ones they love. As morning sets in, Ash is all excited for his training to be strong just like his Pokémon so that they can successfully carry out the transformation. He calls out his flying Pokémon and runs off towards Snowbelle City, prompting Serena, Clemont and Bonnie to follow him, trying to catch up with the excited Ash.