Squishy battles against Z-2 to try and snap it out of Team Flare's control. Meanwhile, Chespie was absorbed by the Megalith Crystal in Lysandre Labs, which transforms into a giant Megalith Zygarde. Dedenne runs off in frustration. With some time left before Ash's return flight to Kanto, he and Clemont have one last Pokémon battle. Ash is able to free himself using his and Greninja's Bond Phenomenon.
Xerosic ends up arrested by law enforcement. This will result in a planetary apocalypse. With no other option, Squishy and Z-2 join forms with every Zygarde Cell in the world to transform into the 100% Zygarde Complete Forme. With Alain's ties to Team Flare revealed, he is forced to take Ash captive. Hoenn Champion Steven Stone and Team Rocket distract most of Team Flare's forces. Alain instantly regrets what he has done after seeing what Team Flare's plans truly are.
Meanwhile, Squishy transforms into the 50% Form to battle Z-2. The Megalith Zygarde was headed towards Anistar City to absorb the power from the Anistar sundial. The battlefield changes to a rock field and Ash substitutes Noivern against Sawyer's Salamence, but both knock each other out. What secret is hidden in the legendary never-before-seen pokémon Zygarde? Serena, Sycamore, and Mairin infiltrate Lysandre Labs to rescue Chespie. Clemont and Clembot are able to get into the Lumiose Gym to destroy Team Flare's control machine.
The Kalos League at Lumiose City finally begins. Ash and Alain continue their battle against Lysandre. . Chaos erupts as Team Flare attacks Lumiose City with Z-2. Squishy shares a tearful goodbye with Bonnie before returning to the planet with Z-2. The Zygarde Complete Forme is able to destroy the Megalith Zygarde and kill Lysandre in a devastating Core Enforcer move.
They were successful in defeating Lysandre. Ash and the gang are at Lumiose airport. Afterwards, more remnant vines and both Zygarde appear. Squishy and Z-2 are released from Team Flare's control. She decides to host a Pokémon Showcase in Lumiose City with help from Shauna and Jessie to cheer everyone up.
Ash defeats Sawyer in the second semi-final match and moves on to the final match against his rival Alain. Ash, Sawyer, Tierno, Trevor, Alain, Remo, and Astrid from Mega Evolution Act 1 are all competing in the Kalos League. Pikachu out-maneuvers and defeats Aegislash. Ash announces his arrival at home in the Kanto region. Ash and Alain get help from former Team Flare member and current Kalos Elite Four member Malva. Serena heads to her flight and gives Ash a kiss before boarding her flight.
What is the mysterious phenomenon that occurs only with Ash's Greninja? As Ash heads to his match, a trainer suddenly challenges him to a battle. Xerosic tries to brainwash Clemont to revive the goals of the now defunct Team Flare, but he fails to do so. Serena, Sycamore, Mairin, and a disguised Team Rocket go to rescue Chespie from Lysandre labs. Bonnie has to find a way to help Squishy. Pikachu loses to Sceptile, but Ash-Greninja wins against Mega-Sceptile. They all allow their Pokémon to say goodbye to each other. The first match is between Alain and Trevor, which sparks a battle between Mega Charizard X and Mega Charizard Y.
Sawyer's Slurpuff faces Ash's Goodra, but it's another double knock-out. Ash, Clemont, Alain, Malva, Steven Stone, the Kalos Gym Leaders, and the Kalos League Champion join forces to defeat the Megalith Zygarde. Ash ends up releasing Greninja in the care of Zygarde to help restore order to the Kalos region. This reveals Squishy's identity as Zygarde to the group. Squishy is put under the same control as Z-2. Having taken it out, Xerosic appears and abducts Clemont. However, Serena is torn on what to pursue next.
Bonnie is able to reach through to Squishy with her lullaby. They realize that Lysandre is taking control of the Megalith Crystal. Ash lends a helping hand to Serena to make a decision. Pikachu defeats Clawitzer, but now faces Aegislash! Ash and Greninja notice that the vine is being fueled by some kind of energy in the ground. The Megalith Zygarde is still able to function without Chespie.
When all the mysteries are revealed, the greatest danger the Kalos region has ever seen will appear! While Lumiose City continues to be repaired, Serena notices its residents are still shaken up by the recent destruction. They team up with a remorseful Alain to battle Team Flare's leader Lysandre. Ash's Pokémon are quickly being overpowered by Lysandre's Mega Gyarados. The Zygarde Complete Forme repairs the damage caused by the battle. After Bonnie convinces Dedenne to return, Serena's flight to the Hoenn region is about to take off. Following Alain's victory over Remo in the first semifinal match, Ash and Sawyer's long awaited battle in the second semifinal match begins in a forest battlefield, with Ash's Hawlucha losing to Sawyer's Slaking and Ash's Talonflame avenging the loss but losing to Sawyer's Clawitzer. Ash and Alain continue their battle against Lysandre.