After seeing the stadium infested with vines, Ash and Alain proceed to leave the stadium, and Alain asks Ash about Mairin's whereabouts. Ash tells him that she didn't want to get in the latter's way, so she asked Ash to not tell him. He then asks Alain if Mairin is important to him; Alain confirms it, and Ash offers help in looking for her. Once they exit the stadium, they meet up with Bonnie, Clemont, and Serena; Bonnie informs Ash that Squishy has wandered off. The group hears an announcement from Malva, addressed to the citizens of Lumiose City, warning them to stay away from Prism Tower due to the danger it possesses. Wondering over the cause of the calamity, the group sees the red Zygarde, and Alain realizes that Zygarde must be behind the plant infestation. Squishy is seen heading to Prism Tower, and absorbs Zygarde Cells to transform into its 10% Forme to increase its speed. Bonnie senses where Squishy is going and runs off to catch up to it. Ash tells Clemont and Serena to go with her and informs them that he is going with Alain to find Mairin. Clemont gives Ash a communicator to keep in touch with him and Serena advises Ash to be careful. Concuurently, Sawyer, Shauna, Tierno and Trevor call out Sceptile, Ivysaur, Blastoise and Charizard respectively to help the citizens to safety from the vines. Professor Sycamore helps get people away from the roots as well, and remembers what Olympia said about the destruction of Kalos, and the role he, along with Ash and his friends, will play to stop the destruction.
Diantha rescues a civilian from the vines with the help of her Gardevoir, before she meets up with Officer Jenny, who informs the Champion that she has assigned her officers with the evacuation of the city, and that the roots are spreading throughout the city; Diantha asks her to lead her to the tower. Meanwhile, Team Rocket tries to fend off the roots with the equipment they are holding, commenting that this is no ordinary disaster. Malva looks at the destruction, and remarks this is Lysandre's doing. Meanwhile, Ash and Alain have caught up with Mairin. Ash informs her that the three need to be going to the Prism Tower. Out of blue, a root spurts up from the ground, but a Dragon Claw from Alain's Charizard destroys it; more vines keep popping up, however, and Ash and Alain try to fend them off with the help of Pikachu and Charizard. Meanwhile, Malva decides to abandon the broadcasting, and informs her assistants that she is going to do something important, telling them to do whatever they want. Jessie gets angry at this sudden abandonment, but then an idea comes across her mind. She informs James and Meowth to get the camera ready, so that she can start broadcasting the entire event all by herself.
Ash and Alain are still busy destroying the roots, when they encounter Celosia, and Ash remembers her as the one hunting for Squishy. She informs Ash that she is not after Squishy this time around, but after him instead. Alain is shocked and confused on Celosia's verdict but she informs him that she is just following Lysandre's orders. Ash asks Alain if he knows the Team Flare scientist but a shocked Alain does not reply. Celosia chimes in, informing a puzzled Ash that she and Alain are colleagues. Ash is shocked to hear that Alain works with the ones chasing Squishy, and inquires Alain about the truth of Celosia's statement, but Alain does not reply him at all. Celosia tells Alain that Lysandre wants to see him, and that an associate of hers is pursuing Squishy. Ash states Alain to ignore Celosia's commands, and tries to leave with him; however, Alain just shrugs his hand off, and Ash is taken aback. The two boys are surrounded by Team Flare Grunts and their Houndour, Celosia commands her Drapion to use Confuse Ray on Ash and Pikachu, causing Ash to faint. Pikachu decides to fight off the Grunts, and tries to intimidate the Grunts by sparking electricity. Unfortunately, this is in vain, and he ends up passing out as well.
Meanwhile, Jessie is still reporting the incident in Lumiose City, but the broadcast is interrupted by Team Flare's transmission, which is subsequently being played on all forms of media throughout the region. The transmission has Lysandre, the leader of Team Flare, declare his decision to remake the world into a place of pure beauty and peace. He adds that Zygarde, the Order Pokémon, is angry with people and Pokémon, for creating a world in which there is not enough for everyone, and thus he wishes to create a world in which only the chosen ones shall live in the bright and hopeful future. The broadcast causes confusion among the people; Mairin is surprised, and wonders why Lysandre would do such a thing. She is approached by a Team Flare Grunt, who informs her that he has orders to take her to Lysandre. Realizing that Team Flare is an evil organization, she tries to resist and refuses to leave, and is rescued by Professor Sycamore. The Grunt tries to force his way, by commanding a Poison Sting from his Skorupi, but the Professor has his Garchomp counteract by using Dragon Claw, and Mairin and Sycamore escape in the smoke produced by the collision of the moves. Meanwhile, Alain is flying in a jet with Team Flare Grunts and an unconscious Ash and Pikachu, towards the Prism Tower. Mairin thanks the Professor for rescuing her and leaves for the Prism Tower with him, for learning more about the calamity.
Having arrived at the Prism Tower, a furious Alain confronts Xerosic and asks him about Zygarde and about Ash's involvment; Xerosic simply states that Lysandre will explain everything. The Team Flare scientist takes Alain to his boss, who calmly asks him what he thinks about the plan and thanks him for completing the Mega Evolution system; he remarks that peace, that he desires, will soon surround Kalos. Concurrently, Squishy has finally made it to the Prism Tower and stares at the red Zygarde at the top. Lysandre notices the destruction caused by Zygarde, and is pleased that the ugliness from the world is slowly disappearing, commenting that the red Zygarde represents all their anger. Alain is shocked at Lysandre's statement, and reasons that destroying the city does not necessarily bring world peace, and that this protection is nothing he was looking for. Lysandre remarks that he shall just protect the chosen ones instead.
Squishy finally climbs atop the Prism Tower, and tries to communicate with Z2, but in vain, as Lysandre senses Z1 among them. Meanwhile, Serena, Clemont and Bonnie are trying to fight off a vine with the help of Braixen and Luxray, but more vines just keep popping up. Two vines sprout up behind the group, but they are destroyed by Clembot and Heliolisk. The group thanks them for their help, and they decide to head towards Prism Tower, when they are attacked by another vine. The vine is subsequently destroyed by Blaziken Mask's Blaziken. Clemont informs him that the Prism Tower is the speculated source of all the chaos, and the latter decides to go there to help. Serena, Clemont and Bonnie wish to go too, but Blaziken Mask deems it to be too dangerous, and asks them to seek shelter instead. The trio is still intent on fulfilling their wish, and Blaziken Mask gives in, while cautioning them to follow behind him at all times.
Squishy tries to reason with Z2, but the latter attacks it with Dragon Pulse. Squishy tries to counter with its own Dragon Pulse, but it is easily overpowered by Z2, being in the 50% forme, and is knocked off the Prism Tower. Having lost all its Cells, Squishy falls on the ground, as Bonnie senses Squishy's pain and remarks that they must hurry. Meanwhile, Alain questions Lysandre if he wished to protect the world as it is, when he talked about strength to protect, but Lysandre comments that there is no point in trying to protect a tomorrow that is worse than today. Lysandre is informed that all the preparations are complete, as Ash and his Pokémon, bound by restraining devices, are lifted in the air, shocking Alain.
The group reaches Prism Tower, and Blaziken Mask has his Blaziken secure an entrance by using Flamethrower, but it is stopped by a Dark Pulse from Aliana's Druddigon; Aliana, together with Bryony, is determined to stop them from entering the Prism Tower. Meanwhile, Ash regains consciousness and tries to break free from the restraining device. He is greeted by Lysandre, who comments that he cannot let Ash escape. Ash notices the red Zygarde, and confronts Alain about all of the chaos, but Lysandre explains to Ash that he may be one of the chosen ones. At the foot of the tower, Bonnie senses Squishy nearby, as the Order Pokémon floats in the air and transforms in its 50% Forme. Bonnie and her friends are surprised to learn that Squishy is also a Zygarde, while Aliana and Bryony seem pleased that the other Zygarde appeared as well, just as Lysandre expected. The red Zygarde jumps from the top of the tower to confront Squishy, which declares that it will use force if the former refuses to listen to it. It then lets out a loud cry before battling Z2.