On their way out of Lumiose City, our heroes visit Professor Sycamore, who enthusiastically shows them his latest experiment: he’s acquired a Key Stone and a Mega Stone, and he wants to see if his friend Garchomp will Mega Evolve! But while everyone’s excitement builds, there is a huge explosion and Garchomp is whisked away, along with both stones. Upon further investigation, the thieves turn out to be none other than Team Rocket!
Professor Sycamore and our heroes chase after them, soon joined by the mysterious man in the Blaziken mask. When Team Rocket tries to get Garchomp to Mega Evolve and join them, the masked man lends the professor his Key Stone. Quickly, the bond between professor and Pokémon overwhelms even Team Rocket’s mind control ray. Mega Garchomp, Blaziken, and Pikachu combine to send the villains blasting off again!
Ash, Serena, Clemont, and Bonnie say their goodbyes and head off toward Laverre City. Meanwhile, the professor seems to have figured out who’s behind the Blaziken mask...
Ash and his friends decide to visit Professor Sycamore before leaving Lumiose City. At that moment, the Professor is having Meyer fix something of his, but soon returns to his research laboratory. When the group arrives at the laboratory, Professor Sycamore and Sophie greets them and shows them his newest research: he has acquired a Key Stone and a Garchompite Mega Stone, meaning that Garchomp can finally Mega Evolve. He also shows the group his Mega Stone synchronizer machine, a device that helps identify the compatibility of a Mega Stone with a specific Pokémon.
However, before anything else can occur, Team Rocket breaks into the laboratory with a Meowth-shaped machine reminiscent of one they used before. They steal the Key Stone, Garchompite, and Garchomp before fleeing in a hurry. Acting quickly, Clemont hands Ash a special device, which Ash throws onto the Meowth machine before it is out of reach. Clemont then pulls out a new invention: a tracking machine that will register the device Ash put onto the mecha. Professor Sycamore drives them all in his car, following the lead provided by Clemont's machine. However, where Team Rocket is located, as Inkay uses Psybeam to free the Garchompite from Professor Sycamore's machine, it destroys the tracker as well and Clemont's apparatus explodes. With their only lead lost, Professor Sycamore climbs out of the car and shouts desperately for Garchomp, hoping she will hear him.
Meanwhile, Team Rocket prepares to attempt to Mega Evolve Garchomp. Meowth turns on special guidance waves to control Garchomp before James lets her out of her cage. Fixing the Garchompite around Garchomp's neck, James proceeds to try and force her to Mega Evolve. With Clemont's device broken, Ash, Professor Sycamore, and the rest of the group continue their search for Garchomp and go to where Clemont last received a transmission from his machine. As they walk, Professor Sycamore reflects on the time when he first met Garchomp, when she was still a Gible - Alain had brought her in when she was rampaging in Lumiose City, and she had gradually learned to trust the Professor and the others before evolving into Gabite and eventually Garchomp. While Team Rocket is controlling her, Garchomp suddenly has visions of those same memories of her time with Professor Sycamore, and the Mega Evolution fails. As Garchomp lets out a howl of distress, Professor Sycamore hears her, despite Ash and the others hearing nothing, and he follows his instinct to lead them to Garchomp.
Team Rocket, frustrated by their failure to Mega Evolve Garchomp, try to figure out the reason. Assuming that Garchomp is refusing to Mega Evolve, Meowth turns up the intensity of the control waves. Seeing the light of Garchomp's attempted Mega Evolution, Professor Sycamore sprints to Team Rocket and tries to stop them from hurting his friend any more. However, as the radio waves begin to hurt the Professor as well, Blaziken Mask appears and uses his Blaziken to stop them. Unfortunately, Meowth is able to restart the transmission of the waves and Team Rocket begins to gain the upper hand again.
In a desperate attempt to stop Team Rocket, Professor Sycamore convinces Blaziken Mask to lend him a Key Stone so that he can Mega Evolve Garchomp before Team Rocket does. Both James and the Professor use their Key Stones, and Garchomp finally achieves her Mega Evolution. When James orders her to get rid of the others, she begins to walk towards Professor Sycamore, but only to embrace him, having broken free of Team Rocket's control. With the boost in her power, Garchomp easily destroys the mecha and sends Team Rocket blasting off with help from Blaziken and Pikachu. Professor Sycamore returns the Key Stone to Blaziken Mask after smelling a familiar fragrance on it, and Blaziken Mask takes his leave when Officer Jenny arrives.
That evening, Ash and his friends leave Lumiose City after thanking Professor Sycamore. The next morning, the professor pays a visit to Meyer at his shop and explains that the smell of the Key Stone was the same smell he had picked up from Meyer earlier. Meyer then agrees that he and Blaziken will assist the Professor with his research on Mega Blaziken.