Heading to the next gym, the gang come across Sawyer again but Bonnie finds an unknown Pokémon in her bag and an evil team is after it.
Serena's Eevee finds itself the unwanted target of a Quilladin as Team Rocket prepare to attack.
The gang come across a Nurse Joy has found an Audinite to Mega Evolve her Audino but Team Rocket hear this.
The gang find a Litleo who after being abused by a Pyroar has run away from its herd.
Squishy rests near a bush unaware that a Darkrai is nearby enveloping it in a nightmare with Pikachu and Meowth being dragged into it.
With the Village of Ninja's under attack, the gang try their best to help but things look helpless until Frogadier begins to evolve.
Serena enters the Couriway Town Showcase keen to win her third key using Eevee in its debut but Nini and Jessie are also entering.
Travelling through Terminus Cave, the gang have another encounter with Team Flare who again target Squishy.
Following the attack from Team Flare, Bonnie is upset are being separated from Squishy and tries to find it.
A gust of wind sends Noibat flying and lands on a Breloom who isn't too happy and leaves Noibat poisoned.
The gang learn from Miette of a dance party taking place for performers and Serena is invited but her hopes of having Ash as her partner are foiled by Miette who asks Ash first.
During a battle with Sawyer, Greninja's transformation is noticed by Alain who is passing and challenges Ash to a battle with his Charizard.
Team Flare are on the hunt to capture Z2 but Team Rocket are tasked by Giovanni to hunt it down and claim it for Team Rocket.
Travelling through a desert, the gang come across a boy and a Chesnaught who are working to plant trees.
Serena hopes to win her third and finally Princess Key in order to go through to the master class but the competition is strong and one trainer has a Shiny Dragonair.
The group find themselves caught in a storm where the legendary Pokémon is on a rampage and medicine is needed to get to a nearby town.
Arriving in a town, the gang come across a jewelry store manager trying to protect his shop from a thief who uses a Binacle to unlock safes.
Serena arrives to take part in the Masterclass Performance but rivals including Jessie, Shauna, Miette and Nini are also taking part.
Serena finds herself along with Shauna and Jessie in the final round of the Master Class where the winner will get to compete against Aria to become Kalos Showcase Queen.
Bonnie's hope of finding a girlfriend for Clemont come true when Clemont finds himself attracted to a girl but as things progress, Bonnie doesn't like it.
A trainer with his own Pikachu learns that Ash also has a Pikachu and wants to battle Ash but Ash is ill so Serena decides to battle for him.
Trying to figure out how to unlock Greninja's new form, Clemont builds an invention to try and unlock some answers when they encounter Alain again who challenges Ash to a battle.
Team Rocket are interrupted by a group of Phantump and get blasted of along with a Shiny Phantump who comes across Ash and friends but can't get back home.
The gang meet up with Kalos Champion Diantha who informs them of Team Flare and the various incidents around Kalos before having a match with Ash and Greninja.
Meeting up with Sawyer again who has got the 8 badges needed to enter the Kalos League, Ash challenges him to another battle against Sceptile, Doublade and Clawitzer.
Keen to win his 8th and final Kalos gym badge, Ash challenges Wulfric to a battle but his Avalugg proves to be tough.
Ash's confidence is low after learning to help perfect Ash-Greninja's form needs strong bond and trust and is out in the winding woods alone leaving the others worried.
Satoshi issues a rematch battle against Urup to obtain his eighth Kalos Gym Badge. He has a big challenge in front of him as he has to battle against Mega Yukinooh. With the help of Satoshi-Gekkouga, Satoshi defeats Gym Leader Urup and receives his eighth and final Kalos Gym Badge.
As Satoshi and his friends continue to the Kalos League, they arrive at the Wetlands to see Numelgon. However, a Melecie goes on a rampage and sparks a search. Meanwhile, Alan battles against Korrina to obtain his eighth Kalos Gym Badge.
Ash and his friends arrive at the Gadget Festival, where many inventions are on display. Clemont is very excited to visit the Gadget Festival. Trouble starts to arise when Team Rocket starts stealing people's Poké Balls.
The Kalos League at Lumiose City finally begins. Ash, Sawyer, Tierno, Trevor, Alain, Remo, and Astrid from Mega Evolution Act 1 are all competing in the Kalos League. The first match is between Alain and Trevor, which sparks a battle between Mega Charizard X and Mega Charizard Y. As Ash heads to his match, a trainer suddenly challenges him to a battle.
Ash defeats Astrid in the quarterfinals and advances onto the semifinals. Meanwhile, the quarterfinal battle between Sawyer and Tierno begins. Sawyer is the winner. The semifinal battles are revealed to be between Alain and Remo and Ash and Sawyer. Ash reveals that his sixth Pokémon will be Goodra.
Following Alan's victory over Louie in the first semifinal match, Satoshi and Shota's long awaited battle begins.
Satoshi-Gekkouga wins against Mega Jukain. Satoshi moves on to the final match against his rival Alan.
While Satoshi prepares for his final match against Alan in the Kalos League, he meets Flare-Dan's boss Fleur-de-lis. Meanwhile, Citron's Harimaron gets lost and meets Manon.
The final match between Satoshi and Alan in the Kalos League begins.
The final match between Alan and Satoshi ends with Alan announced as the victor of the Kalos League. Meanwhile, Flare-Dan prepares to move forward with their plans to control Z-2 in Miare City.
Chaos erupts as Flare-Dan attacks Miare City with Z-2. Z-2 causes widespread destruction. With Alan's ties to Flare-Dan revealed, he is forced to take Satoshi captive. Alan instantly regrets what he has done after seeing what Flare-Dan's plans truly are. Meanwhile, Puni-chan transforms into the 50% Form to battle Z-2. This reveals Puni-chan's identity as Zygarde to the group.
Puni-chan battles against Z-2 to try and snap him out of Flare-Dan's control. Puni-chan is put under the same control as Z-2. Citron and the rest of the heroes battle against Flare-Dan's executives. Serena, Plantane, Manon, and a disguised Rocket-Dan go to rescue Harimaron from Fleur-De-Lis labs. Satoshi is able to free himself using his and Gekkouga's Bond Phenomenon and team up with a remorseful Alan to battle Flare-Dan's leader Fleur-De-Lis.
Satoshi and Alan continue their battle against Fleur-De-Lis. Satoshi and Alan's Pokemon are quickly being knocked out by his Mega Gyarados. Satoshi and Alan get help from former Flare-Dan member Pachira. Citron and Citroid are able to get into the Miare Gym to destroy Flare-Dan's control machine. Citron and Citroid are able to do so, but Citroid is destroyed in the process. Serena, Plantane, and Manon infiltrate Fleur-De-Lis Labs to rescue Harimaron. Hoenn Champion Daigo Tsuwabuki and Rocket Dan distract most of Flare-Dan's forces. Eureka is able to reach through to Puni-chan with her lullaby. Puni-chan and Z-2 are released from Flare-Dan's control.
Satoshi and Alan continue their battle against Fleur-De-Lis. They were successful in defeating Fleur-De-Lis. Meanwhile, Harimaron was absorbed by the megalith crystal in Fleur-De-Lis Labs, which transforms into a giant Crystal Zygarde. The Crystal Zygarde was headed towards Hyakkoku City to absorb the power from the Hyakkoku sundial. This will result in a planetary apocalypse. Satoshi, Citron, Alan, Pachira, Daigo, the Kalos Gym Leaders, and the Kalos League Champion join forces to defeat the Crystal Zygarde.
As the Kalos Gym Leaders are trying to stop the crystal, Satoshi and Alan are successful in saving Harimaron. The Crystal Zygarde is still able to function without Harimaron. They realize that Fleur-De-Lis is taking control of the crystal. With no other option, Puni-chan and Z-2 join forms with every Zygarde Cell in the world to transform into the 100% Zygarde Complete Form. The Zygarde Complete Form is able to destroy the Crystal Zygarde and hug Fleur-De-Lis in a devastating Core Enforcer move. The Zygarde Complete Form repairs the damage caused by the battle. Puni-chan shares a tearful goodbye with Eureka before returning to the planet with Z-2.
Citron successfully repaired Citroid. Due to Citroid's memory core being destroyed, it has no memory of its past and consequently no experience. Meanwhile, a returning Pokémon trainer asks for a rematch with Citroid.
While Miare City continues to be repaired, Serena notices its residents are still shaken up by the recent destruction. She decides to host a TriPokalon in Miare City with help from Sana and Musashi to cheer everyone up. However, Serena is torn on what to pursue next. Satoshi lends a helping hand to Serena to make a decision.
Heading back to Lumiose airport after saying goodbye to Goodra, Ash and the gang encounter a remnant vine from the attack. Ash and Greninja notice that the vine is being fueled by some kind of energy in the ground. Having taken it out, Xerosic appears and abducts Clemont. Xerosic tries to brainwash Clemont to accomplish the goals of Team Neo Flare, but he fails to do so. Xerosic ends up arrested by the police. Afterwards, more remnant vines and both Zygarde appear. Ash ends up releasing Greninja in the care of Zygarde to help restore order to Kalos.
Ash and the gang are at Lumiose airport. They all allow their Pokémon to say goodbye to each other. Dedenne runs off in frustration. After Bonnie convinces Dedenne to return, Serena's flight to the Hoenn region is about to take off. Serena heads to her flight and gives Ash a kiss before boarding her flight. With some time left before Ash's return flight to Kanto, he and Clemont have one last Pokémon battle. Ash announces his arrival at home in the Kanto region.
Professor Sycamore investigates the origins of the XYZ legend with Alexa about the story of a man named Jan and his love interest named Aira. A prophecy made long ago predicted that Yveltal would appear and drain all life from Kalos. Upon the arrival of Yveltal, Aira becomes fossilized as a statue while defending Jan. Afterwards, Yveltal enters into its long term sleep. Jan searches out Xerneas to restore life to Kalos. Years later, Xerneas reappears and does so. However, Aira is left as a statue. Many years later, Jan can be seen as an old and blind man. Jan discusses how he sleeps in the same spot every night. Jan talks to the Aira statue about how Xerneas and Zygarde made the forest so beautiful. Jan cuts an image of the "Z" symbol for Zygarde with a Zygarde Cell on it. Jan falls asleep for the last time. Jan says, "I want to be with her. I will sleep a little".