With Pyroar taken down, Ash commands his Noivern and Pikachu to use Boomburst and Thunderbolt, respectively, on Lysandre's Mega Gyarados, but the Atrocious Pokémon counters with Hyper Beam; it uses Dragon Tail to attack Pikachu but Noivern pushes him aside and takes the hit, knocking him out. Alain's Mega Charizard X attacks the Atrocious Pokémon with Dragon Claw and Hawlucha follows up High Jump Kick, but Mega Gyarados clutches the Wrestler Pokémon's wing with its mouth, and throws him away, successfully knocking him out. Lysandre explains that Mega Evolution is a battle instinct, and that Pokémon have forgotten its essence since interacting with humans; for a Pokémon to gain Mega Evolution power, it is a must for it to unleash its battle instinct. Alain, of course, disagrees with him, but Lysandre simply claims that only the victor can prove that he is not wrong, and commands Mega Gyarados to use Hyper Beam. Meanwhile, Bonnie is still trailing Squishy, and is stopped by Blaziken Mask. She asks him to let her go so that she may save Squishy. Blaziken Mask is still indecisive, but Bonnie frees her hand and starts following the Order Pokémon.
Inside the Lumiose Gym, Clembot has successfully found the right code to open the door, and the noise from the opening of the door alerts two Team Flare Grunts working on the Zygarde control device. Clembot suggests infiltrating Team Flare's system to stop it from working, and free the red Zygarde. Clemont's Luxray uses Electric Terrain to knock the two grunts out. Attracted by the sounds, Xerosic shows up in front of Clemont, who asks if he is the one controlling Zygarde with the device. and Xerosic agrees, declaring the Zygarde control device to be his greatest invention. Clemont does agree, and explains that devices that control Pokémon and cause destruction are not worthy of being called inventions. Xerosic is not pleased, and calls out his Malamar and Crobat to challenge Clemont's belief. He commands his Pokémon to use Psycho Cut and Air Slash respectively, but they are countered by Bunnelby's Mud Shot and Chespin's Pin Missile, as Clembot silently reaches the device, and starts its infiltration.
Team Rocket's helicopter is nearing Lysandre Labs; awaiting their arrival, Mable commands her Weavile to attack it with Ice Shard. Serena and Braixen decide to fight back, with Flamethrower to counter another Ice Shard. However, an Icy Wind directly connects with the helicopter, and causes it to malfunction. However, the Sharp Claw Pokémon is stopped from continuing its attack as it is hit by a Flash Cannon from Steven Stone's Mega Metagross. Steven Stone climbs off his Metagross to confront Mable and commands his Pokémon to use Meteor Mash, which is narrowly avoided by Mable and her Weavile. Steven expresses his feelings on being fooled by Lysandre, but Mable disagrees and states that this is just an undertaking to create a beautiful world. Team Flare Grunts appear on the site, as she proposes Steven to side with Team Flare, but Steven does not relent. Having gotten off the helicopter, Mairin and Professor Sycamore greet the Hoenn Champion, and the latter informs him about Chespie and the Giant Rock inside the Lysandre Labs. James is surprised by the sudden appearance of the Champion, but the infatuated Jessie is bothered only about filming him, causing her to be chided by Meowth and Wobbuffet. Steven asks Mairin, Sycamore and Serena to continue their quest, as he proceeds to battle the Team Flare members.
Inside Lysandre Labs Mairin, Serena and Sycamore scramble towards the room where Chespie is being kept, with Team Rocket filming the entire event, when they are suddenly attacked by a Sludge Bomb from Celosia's Drapion. Team Rocket is angered due to the surprise attack, and remove their disguises to reveal their identity to the Team Flare scientist. Serena is surprised, and the trio tells them to rush and rescue Chespie. James remarks that they have no intention to hand over the world to them, and calls out his Inkay to attack with Psybeam, just as Jessie calls out her Gourgeist to use Seed Bomb, but their moves are canceled by Drapion's Sludge Bomb. Meanwhile, Alain's Mega Charizard X attacks Mega Gyarados with Thunder Punch, and Ash has his Goodra attack it with Dragon Pulse; Mega Gyarados counteracts with Hyper Beam, and knocks the Dragon Pokémon out. Lysandre chides Ash for losing three of his Pokémon so soon, but Ash claims that he will not quit; he remarks that in addition to their fighting spirit, a Pokémon's strength is highly determined by the bond between it and its Trainer. To prove his point, he has his Talonflame and Greninja use Flame Charge and Cut, which Mega Gyarados easily counters with Stone Edge, sending the two flying who are rescued by Charizard. Mega Gyarados follows up with Dragon Tail, smashing the three on the floor and knocking Talonflame out. Lysandre is pleased, and commands his Mega Gyarados to use Hyper Beam on the group, which is countered by a Flamethrower from Malva's Mega Houndoom. The Elite Four member claims that the time has come to put an end to the destruction caused by him. Lysandre is surprised by her sudden switching sides, but she explains that she is just putting her complete trust in the kids. She admits that while she is not satisfied with the world as it is now, watching Alain and Ash inspires her and convinces her that as long as they, the adults, are able to teach the younger generation to lend a helping hand, the future is worth fighting for. Lysandre is disappointed and rebuffs her. He commands Mega Gyarados to use Incinerate, which is canceled by Water Shuriken. Ash repeats his stance, claiming that he is fighting for the tomorrows of people and Pokémon who call the world their home. Malva supports Ash for this belief of his, but Lysandre simply dismisses this as naivety.
Mairin and Sycamore have finally reached Chespie's room, and Sycamore decides to take the sick Pokémon to his laboratory. Outside, Serena and her Pokémon are outnumbered by Team Flare Grunts and their Houndoom. While they think of a way to escape, Steven and his Metagross show up, and aid them by causing the grunts to levitate with Psychic. Meanwhile, Blaziken Mask, Mega Blaziken and Bonnie rush past Squishy and stand in its way, so that Bonnie can confront it. Bonnie tries to calm it down and claims that everything is fine. Squishy, however, is unaffected by her pleadings and attacks her with a vine, which is taken by Blaziken Mask instead. Seeing that Squishy does not even recognize her anymore, Bonnie gets overwhelmed with sadness and starts singing Puni-chan's Song in a feeble and sad voice as her tears start to fall. Squishy approaches Bonnie as Dedenne tries to comfort her, but slows down when it hears the song, but is still ready to attack and lifts some vines in air. However, as it does so, its eye begins to light up as if fighting an internal battle with itself. Sensing danger, Mega Blaziken and Dedenne stand in front of Bonnie to protect her, as Bonnie sings louder upon realizing the song is getting through to Squishy. As she continues singing, Squishy begins charging a Dragon Pulse, but as it does so the light begins to light up faster. Blaziken Mask recovers and attempts to shelter Bonnie as she continues her singing. Squishy fires the Dragon Pulse as Bonnie completes her song, but the move is redirected at the last second to avoid Bonnie and hits a building, causing debris to fall over the group. Fortunately, the group is protected from harm by Squishy which has now broken free of Team Flare's control and has returned to its senses, restoring it to its natural green color. An overjoyed Bonnie strokes Squishy affectionately, as it splits up from its Cells. Atop the Prism Tower, Lysandre contacts Xerosic to know the reason for the splitting, but the latter simply shuns him, claiming that he is too busy battling an intruder, the Gym Leader, Clemont. An exhausted Squishy falls into Bonnie's arms, and Bonnie is glad at Squishy's safety.
Inside the Lumiose Gym, Clemont successfully defeats Xerosic, and Clembot has completely taken control of Team Flare's system. Xerosic attempts to regain control over his device, but ends up being thrown out of the Gym through the trapdoor. Clemont decides to synchronize Clembot with the system, but stops upon realizing that forcing the device to shut down will cause Clembot to lose all of its main memory. Clemont is hesitant to do such a thing that would be detrimental to Clembot, but Clembot reasons that being the generous Gym Leader of Lumiose City as he is, Clemont must consider the well being of the many instead of just one. A tearful Clemont realizes his responsibility and works on Clembot's internal computer to trigger the program that will shut down the device; however, he hesitates to initiate the shutdown process. Clembot encourages him to do the right thing, claiming that he is the one who can save the world. Clembot thanks him for creating it, as an overwhelmed Clemont gathers all his might through his conflicting emotions, and initiates the shutdown process to cause the device, and along with it, Clembot, to start short-circuiting and breaking down. As a consequence of his actions, Z2 snaps out of Team Flare's control, and starts to split up. Depressed over his actions, Clemont cries on the heavily damaged body of Clembot as Chespin tries to comfort him. Malva notes that Z2 has broken free from the control as well, causing Ash to exclaim that Team Flare is done for good. Lysandre, however, is amused by Ash's words, and Mega Gyarados lets out a loud cry.