Clemont, Clembot and Blaziken Mask battle against Team Flare's executives. Ash, Clemont, Alain, Malva, Steven Stone, the Kalos Gym Leaders, and the Kalos League Champion join forces to defeat the Megalith Zygarde. Sawyer's Slurpuff faces Ash's Goodra, but it's another double knock-out. Squishy battles against Z-2 to try and snap it out of Team Flare's control. Squishy is put under the same control as Z-2. Ash and the gang are at Lumiose airport. What secret is hidden in the legendary never-before-seen pokémon Zygarde? Ash defeats Sawyer in the second semi-final match and moves on to the final match against his rival Alain.
Squishy and Z-2 are released from Team Flare's control. They were successful in defeating Lysandre. Squishy shares a tearful goodbye with Bonnie before returning to the planet with Z-2. Xerosic ends up arrested by law enforcement. The Megalith Zygarde was headed towards Anistar City to absorb the power from the Anistar sundial. What is the mysterious phenomenon that occurs only with Ash's Greninja? Hoenn Champion Steven Stone and Team Rocket distract most of Team Flare's forces.
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. Meanwhile, Squishy transforms into the 50% Form to battle Z-2. Ash is able to free himself using his and Greninja's Bond Phenomenon. Ash's Pokémon are quickly being overpowered by Lysandre's Mega Gyarados. . Alain instantly regrets what he has done after seeing what Team Flare's plans truly are. Serena heads to her flight and gives Ash a kiss before boarding her flight.
She decides to host a Pokémon Showcase in Lumiose City with help from Shauna and Jessie to cheer everyone up. Chaos erupts as Team Flare attacks Lumiose City with Z-2. Afterwards, more remnant vines and both Zygarde appear. Heading back to Lumiose Airport after saying goodbye to Goodra, Ash and the gang encounter a remnant vine from the attack. Pikachu loses to Sceptile, but Ash-Greninja wins against Mega-Sceptile. The Zygarde Complete Forme is able to destroy the Megalith Zygarde and kill Lysandre in a devastating Core Enforcer move. As the Kalos Gym Leaders are trying to stop the Megalith Crystal, Ash and Alain are successful in saving Chespie.
With Alain's ties to Team Flare revealed, he is forced to take Ash captive. They realize that Lysandre is taking control of the Megalith Crystal. Ash announces his arrival at home in the Kanto region. Ash and Alain continue their battle against Lysandre. Bonnie is able to reach through to Squishy with her lullaby. Pikachu defeats Clawitzer, but now faces Aegislash! However, Serena is torn on what to pursue next. What is the aim of Alain and Team Flare, who stands in the way of Ash and his friends? Ash lends a helping hand to Serena to make a decision.
Ash ends up releasing Greninja in the care of Zygarde to help restore order to the Kalos region. The battlefield changes to a rock field and Ash substitutes Noivern against Sawyer's Salamence, but both knock each other out. The Megalith Zygarde is still able to function without Chespie. Ash and Alain get help from former Team Flare member and current Kalos Elite Four member Malva. 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. This reveals Squishy's identity as Zygarde to the group.
Ash and Alain continue their battle against Lysandre. The Zygarde Complete Forme repairs the damage caused by the battle. 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. Meanwhile, Chespie was absorbed by the Megalith Crystal in Lysandre Labs, which transforms into a giant Megalith Zygarde. They team up with a remorseful Alain to battle Team Flare's leader Lysandre.
Having taken it out, Xerosic appears and abducts Clemont. While Lumiose City continues to be repaired, Serena notices its residents are still shaken up by the recent destruction. Ash, Sawyer, Tierno, Trevor, Alain, Remo, and Astrid from Mega Evolution Act 1 are all competing in the Kalos League. Bonnie has to find a way to help Squishy. Pikachu out-maneuvers and defeats Aegislash.
After Bonnie convinces Dedenne to return, Serena's flight to the Hoenn region is about to take off. As Ash heads to his match, a trainer suddenly challenges him to a battle. The first match is between Alain and Trevor, which sparks a battle between Mega Charizard X and Mega Charizard Y. When all the mysteries are revealed, the greatest danger the Kalos region has ever seen will appear! Clemont and Clembot are able to do so, but Clembot is destroyed in the process. The Kalos League at Lumiose City finally begins.