Squishy and Z2 are facing each other down, ready to commence their battle, as Ash is surprised to learn that Squishy is Zygarde. Lysandre explains that Zygarde watches over the the world, punishing those who dare to disrupt its order. He adds that the rage of Zygarde, as well as Team Flare, will cause the world to end, and a new age to begin. Alain is shocked to hear such words from the Team Flare Boss, who comments that Squishy shall also accept their way of thinking, and turn red with rage. A captured Ash rebukes Lysandre for thinking so, and demands an explanation from Alain. Meanwhile, Jessie is seen reporting the calamity on a news helicopter, and comments on the presence of the two Zygarde in the center of Lumiose City.
Squishy lets out a loud cry, and slams Z2 into a building, worrying Bonnie. Bryony asks her and her friends to not get distracted, as Aliana commands her Druddigon to use Dark Pulse. However, the attack is stopped by Professor Sycamore's Mega Garchomp. Professor Sycamore is glad to have made it in time, as Mairin notifies him about the two battling Zygarde. A worried Bonnie asks Z2 to listen to Squishy, while the Team Flare scientists claim that beating Mega Evolved Pokémon might be challenging. Bryony commands her Liepard to use Shadow Claw, but it is countered by Mega Blaziken's Blaze Kick. Clemont calls out Bunnelby and Chespin for help as well, and commands his Luxray to use Wild Charge, which misses. Chespin then uses Pin Missile while Clembot commands Heliolisk to use Dragon Tail, but Liepard and Druddigon avoid the attacks. Liepard uses Dark Pulse, but it is countered by a Mud Shot from Bunnelby. Blaziken Mask has his Mega Blaziken use Flamethrower, but Druddigon avoids the attack, and damage with Dragon Claw. Meanwhile, Mairin asks Serena if she has seen Alain and Ash, but she is replied in the negative. Serena tries to comfort Mairin, but after realizing that she is worried for her Chespie, decides to rescue the Spiny Nut Pokémon from Lysandre Labs, together with Mairin and Sycamore. The three narrowly avoid a Dark Pulse, with Bryony claiming that they refuse to be ignored. She has her Liepard use Shadow Claw, but the Cruel Pokémon is hit by a Mud Shot. Clemont signals the three to go, and warns the Team Flare scientists that they are up against the Gym Leader of the Lumiose Gym. Meanwhile, Team Rocket decides to infiltrate the Lysandre Labs to bring the organization down.
At the top of the Prism Tower, Lysandre thanks Alain for his efforts, as he reveals that Mega Evolution energy has given them the power to control Zygarde, shocking both him and Ash. He claims that the Mega Evolution energy is quite useful in destroying the imperfect world, and that the next sunrise shall mark the beginning of the new and beautiful world, a world full of peace. Hearing this, Alain is shattered, and falls on his knees, and he repeatedly slams his fist on the floor in anger and disappointment. Ash realizes that Alain collected all the energy for Chespie's sake, which is further backed by Lysandre, who remarks that Alain's wish had pure intent.
Continuing towards Lysandre Labs, Serena, Mairin and Professor Sycamore meet up with Team Rocket, who in their disguise, introduce themselves as members of Lumiose TV. They offer to take the three to Lysandre Labs in their news helicopter, and the three gladly take on the offer. Meanwhile, Bonnie notices Z2 attack Squishy with vines, but Squishy easily evades them, and attacks Z2 with Extreme Speed. Squishy, however, is overwhelmed and knocked back. Dedenne suggests Bonnie to go towards Squishy and she runs off towards it. Concurrently, Diantha and her Gardevoir are rescuing the citizens from the vines, when they are approached by Sawyer, Shauna, Tierno and Trevor, who are eager to help in the catastrophe. Diantha accepts their offer, and asks them to rescue and bring children and the elderly to the site, which they happily accept.
In the news helicopter, Team Rocket is very glad, and excited at the success they would have in Kalos if they manage to take control of Team Flare's base. Meanwhile, Z2 knocks Squishy towards a building, which then proceeds to attack the former with Extreme Speed, but is overwhelmed, and bound by Z2's vines. Xerosic laughs at the sight, and exclaims that it wouldn't be long under Squishy falls under their influence as well. At the Prism Tower, Lysandre informs Ash about his interest in the Bond Phenomenon that he and his Greninja can use to achieve new powers, and attempts to control the two with one of Team Flare's devices, wishing to take the power for himself. Ash and Greninja enter a trance when the device hits them, with Pikachu and the others watching in horror for their friends, while Alain asks Lysandre to stop. However, Pikachu's voice gets through to Ash, which helps him and Greninja snap out of their trance and return to their senses. Lysandre tries to reason with Ash, informing him that he shall serve as a guide to humanity in the new world. Ash, however, refuses to succumb, and asks Alain to put a stop to what's currently happening; he states that he does not care what Alain has done, and that he believes in the Alain he knows. He adds that he really cares about the world, and the people and Pokémon who call it home, and refuses to let the world be destroyed. These feelings of his seem synchronize with those of Greninja, and the two undergo Bond Phenomenon to successfully break through their restraining cuffs. Ash is exhausted due to breaking through his restraining cuffs, but Alain comes to aid him. Lysandre is dazzled by the spectacular exhibition of Bond Phenomenon, as he claims that even Mega Evolution could not overpower Ash and Greninja's bond. Alain thanks Ash for clearing him of his confusion, and calls out Charizard to put an end to the chaos and destruction caused by Lysandre. Charizard uses Dragon Claw to destroy the restraints of Ash's other Pokémon. Lysandre is disappointed by Alain's betrayal; he claims that they would never be able to beat him and that none of them shall be needed in the new world. Having put on his equipment, he seems ready to put a stop to the two Trainers and challenges them to a battle.
Down at the base of the Prism Tower, Aliana and Bryony command Druddigon and Liepard to use Dragon Claw and Shadow Claw respectively, but Heliolisk uses Flash to blind them. A barrage of attacks from Luxray, Bunnelby and Chespin causes the two scientists to recall their exhausted Pokémon, and Clembot successfully captures the two Team Flare members, who blame each other for their loss. Bonnie finally reaches the site of the two battling Zygarde, and notices Xerosic attacking the bound Squishy with a beam. Out of blue, Bonnie is attacked by vines, and is saved in the nick of time by Mega Blaziken; she informs Blaziken Mask that she suspects that Squishy is going to lose. Bonnie holds her ears in pain as she hears Squishy's cries, which has finally succumbed to Team Flare's control. Lysandre is informed about the success, who is pleased that his beautiful world shall be created at a much faster pace. Ash is disappointed by the current way of events, and chides Lysandre for believing that his actions are creating peace. Lysandre, however, claims that Ash is just oblivious of the ugly parts of the world. He then explains that he once had a generous nature and would help those in need, but after those he supported grew accustomed to his aid and turned greedy, he became disillusioned with the human race. Because of this, he intends to "restart" the world before the arrogant and foolish people cause about their own destruction with their entitlement. He claims that Ash, Alain, and their Pokémon have no space in his utopia, as he sends out his Pyroar and Shiny Gyarados. Lysandre then uses his ring, containing a Mega Stone, to Mega Evolve Gyarados. Alain responds by immediately Mega Evolving Charizard, and both the sides are ready to battle. Meanwhile, at the Lysandre Labs, Mable and Celosia notice the news helicopter approaching on their screen, and decide to confront the intruders. Inside the Prism Tower, Clemont tries to breach through a door, but he cannot find the correct lock code, when Clembot tries to help and proceeds to analyse all of the possible codes.
Lysandre begins the battle by commanding Pyroar and Gyarados to use Incinerate, but Ash counters by having Pikachu and Goodra use Thunderbolt and Dragon Pulse respectively. Greninja follows up with Cut, but Pyroar uses Hyper Beam to attack, which is countered by Noivern's Boomburst. Alain's Charizard uses Dragon Claw, but Gyarados uses Stone Edge to hit the Flame Pokémon. Noivern and Hawlucha use Dragon Claw and Karate Chop next; Pyroar counters with Fire Fang, but he is successfully hit by Karate Chop and Pikachu's Thunderbolt. Meanwhile, Squishy is wrecking havoc in Lumiose City with vines, and is followed by Bonnie. Lysandre recalls his Pyroar, while Ash claims that Squishy will be rescued, and that his selfishness will not destroy the world.