Ash and Sawyer meet up for a battle, and Greninja and Sceptile, now evolved, are excited for their rematch! Nearby, Alain, who’s on a journey to study Mega Evolution, pauses to watch the battle, and he’s very intrigued when Greninja seems to transform just before defeating Sceptile.
Alain wants to see more of what Ash’s Greninja can do, so he challenges it to a battle against his Charizard—and when Charizard Mega Evolves and Greninja’s appearance changes again, the battle becomes intense! Greninja is ultimately defeated, but everyone is eager to learn more about this mysterious transformation!
Meanwhile, Team Flare’s experiments seem to have reached a breakthrough...
The episode begins with a battle between Ash's Hawlucha and Sawyer's Shelgon, and Hawlucha quickly takes Shelgon out with a Flying Press. Sawyer then sends out his newly obtained Honedge. After Ash scans it with his Pokédex, he sends Pikachu to battle it. After Honedge attacks with Fury Cutter, Pikachu counters with Iron Tail and takes Honedge out with Thunderbolt. Down to his last Pokémon, Sawyer sends out his Sceptile, revealing his Grovyle had evolved. Seeing this, Ash sends out his Greninja, revealing that to Sawyer his Frogadier had also evolved. After Serena scans Sceptile with her Pokédex, the third and final battle begins. Sceptile starts off with Bullet Seed, which is intercepted with Greninja's Water Shuriken. Sceptile quickly gets the advantage after it avoids Cut and counters Aerial Ace with Leaf Blade, creating an impact that catches the attention of Alain after he is alerted a Pokémon with Mega Evolution potential is in the area. Sawyer commands Sceptile to use Dragon Pulse, which successfully connects after Greninja dodges it the first time and then orders Leaf Storm, dealing a lot of damage to Greninja as it is trapped in a cyclone as Ash is forced to watch just as Alain arrives. Sawyer orders Sceptile to slam Greninja onto the ground, but Ash shouts to Greninja, who then transforms into its Ash-Greninja form, much to Sawyer and Alain's surprise, as Alain looks at his Mega Ring, which doesn't react to Greninja's transformation. Ash quickly orders Aerial Ace, which knocks out Sceptile in one hit, slamming it into the wall. Greninja reverts back to normal and Ash and Greninja both fall to the ground exhausted as Ash says it was a good battle. Sawyer, although disappointed that he is still unable to defeat Ash, notes that he has gained a lot of experience. Turning to Ash, he asks about Greninja's transformation, which Ash replies that he has no idea what it even is, but that things flash before him when it happens. Sawyer replies that he understands, but then immediately shouts that he doesn't. As Sawyer yells, Alain stares at Ash and Greninja in awe, his lip quivering in shock.
At the Pokémon Center, Ash and Sawyer take back their Pokémon from Nurse Joy just as Alain arrives, who hands Nurse Joy a Poké Ball. The group sit down as Sawyer asks Ash questions about Greninja's transformation, to which Ash is unable to provide detailed answers to these questions, as Team Rocket listen in on their conversation. Sawyer theorizes that Ash may actually be becoming Greninja, and vice versa, when this change occurs, much to Ash's surprise and delight.
The scene changes to Lysandre Labs where Lysandre is talking to Alain about the Mega Evolution data. Alain then asks about Mairin and Chespie, but Lysandre replies that there has been no change as Mairin is shown with a still comatose Chespie.
Back at the Pokémon Center, Ash and his friends say good-bye to Sawyer, while Alain enters the Pokémon Center as the sun sets.
With night time now upon them, the scene changes and shows Team Flare on an island, operating a machine containing various Zygarde Cells. After being given the all clear by one of the Team Flare Admins, Xerosic orders them to fire a beam, which causes a mutation in the trees, creating much larger, red trees.
As the sun starts to rise in the following morning, Ash and his friends are still sleeping in their room at the Pokémon Center. A shadow is seen on the curtain and a large, mechanical hand smashes through the window and grabs Pikachu, waking everyone up as Ash rushes onto the balcony noticing it was Team Rocket. Ash tells Pikachu to use Thunderbolt to break free, but it proves to be useless as Team Rocket attempts to make their escape with their captive enemy. Ash slides down a nearby lamp post and chases after Team Rocket. Noticing this, Jessie and James send out Gourgeist and Inkay to slow him down and attack with Psybeam and Shadow Ball, but Ash jumps out of the way and makes sure his friends aren't hurt. Clemont quickly warns Ash to look out as Gourgeist uses Dark Pulse, but a Steel Wing attack counters it. Looking up, Ash notices a Charizard and a mysterious looking trainer with a Mega Ring. Charizard uses Dragon Claw to break Pikachu out of the mechanical hand, to which Ash orders Pikachu to use Thunderbolt to send Team Rocket blasting off. Alain quickly orders Charizard to catch Pikachu, which it does and Pikachu is returned to Ash safely. Ash thanks Charizard and notices it has a Mega Stone. Alain tells Ash that he was impressed by Pikachu's Thunderbolt and that he wants to have a battle against Greninja with Charizard, to which Ash accepts.
Ash and Alain prepare to start their one-on-one battle as they send out their Pokémon, with Clemont acting as the referee. As the battle begins, Ash starts off by commanding Greninja to use Water Shuriken, but it is quickly countered by Charizard's Dragon Claw. Ash then orders it to use Cut, but Charizard speedily dodges before being ordered to use Flamethrower, dealing a lot of damage to a vulnerable Greninja. Seeing the perfect time, Alain Mega Evolves his Charizard into Mega Charizard X, which amazes Ash at the sight of Mega Evolution, as well as his friends admiring this. Alain then tells Mega Charizard X to use Dragon Claw, but it is countered by Greninja's Cut, Ash then attempts to confuse Mega Charizard X by having Greninja use Double Team, but Alain quickly commands Mega Charizard X to use Flamethrower, which it uses to destroy the copies and creating a smoke cloud. Using the smoke, Ash commands Greninja to use Aerial Ace, but Mega Charizard X hits it with a powerful Thunder Punch, sending Greninja flying and covered with electricity. Seeing the battle coming to an end, Alain orders Mega Charizard X to use Thunder Punch again as Ash commands Water Shuriken, but Mega Charizard X was faster and hit it once again with a super-effective Thunder Punch, sending Greninja flying again. Ash calls out to Greninja to see if it is alright as Alain watches, waiting to see what happens. Ash tells Greninja that they can't give up and Greninja stands, which then leads to Greninja transforming into Ash-Greninja once again, leading Alain to check his Mega Ring again, unable to understand why it wasn't reacting to Greninja's "Mega Evolution", and how Ash achieved it without a Mega Stone or Key Stone. Ash orders Greninja to use Aerial Ace as Alain tells Mega Charizard X to get above Greninja, but doesn't do much good as Greninja jumps up and delivers the attack. Attempting to get the upper-hand, Alain tells Mega Charizard X to use Thunder Punch, but Ash quickly orders Greninja to use Cut to counter, after the two attacks collide, Alain commands Mega Charizard to use Blast Burn, which connects with Greninja, knocking it out, making Alain the winner as Ash falls to the floor from exhaustion.
Mega Charizard X returns to its normal form and looks as though it was happy about the battle, which makes Alain smile. Ash approaches Greninja to make sure it is alright, and tells Alain that it was a good battle as he looks to Greninja, who agrees with him. Ash introduces himself to Alain and asks who he is, to which Alain introduces himself to Ash as they both shake hands.
Back at the Pokémon Center, Ash is thinking about the battle as Clemont arrives with drinks. Alain is shown continuing his journey as Team Flare is shown standing on the island with the mutated trees as a plane flies to the island.