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Chronologically, this arc takes place at an unknown period.
- Main article: Pokémon Adventures: Volume 1 (XY)
Y, a Sky Trainer, attempts to get X, her childhood friend, to get out of his house. X refuses, since he is still depressed from the "accident" at the tournament he participated in. Suddenly, two legendary Pokémon appear in Vaniville Town and attack each other, causing the town to be destroyed. X and Y, however, face some people, dressed in red clothes and are attacked. X, however, triggers his Key Stone and manages to empower his Kangaskhan with new power and defeat the people in red. With their friends, Tierno, Trevor and Shauna, X and Y go from Vaniville Town. However, they are still chased by the people in red and are being tricked by an innkeeper, so X and Y order Trevor's Pokémon (whom he obtained from a professor), a Froakie and a Chespin, and defeat the people in red - Bryony and Mable. After arriving into Santalune City, Shauna leaves her friends, since they trust Viola, a woman they met in Vaniville Town, before it got destroyed. In order to get the Key Stone, one of the people in red hypnotizes Shauna to obtain X's stone. However, the woman is stopped by Korrina, who, like X, uses the Key Stone to Mega Evolve her Lucario, causing the woman in red to retreat.
- Main article: Pokémon Adventures: Volume 2 (XY)
The group arrives to Lumiose City, where Trevor's net friend, Professor Sycamore, is living. Just before they arrive, they save a Charmander, who nearly burned a whole flower field. The group arrives at the lab, where X has a battle with Professor Sycamore and manages to befriend Chespin and Charmander. Elsewhere, the rest of the group goes to a cafe, where they encounter Lysandre, who is going to repair Trevor's HoloCaster. Trevor fears Lysandre had some part of the accident at Vaniville Town, especially when Lysandre wants to see the pictures Trevor took. However, Diantha, a famous actress, arrives and protects the children, dismissing Lysandre. The group re-unites with X and they go to the Prism Tower, where Alexa, Viola's sister, which the group encountered in Vaniville Town, has her report on Vaniville Town destroyed by her boss, who kidnaps her Helioptile. X manages to save Alexa's Helioptile with Kangaskhan, Chespin and Charmander. After leaving Lumiose City, the group encounters Clemont and an Electrike, who wishes to obtain a Mega Stone. The Electrike evolves into a Manectric, but the Mega Stone is taken by a Team Flare grunt. X fights and manages to evolve Manectric (and befriend it), defeating the grunt. Afterwards, X and Trevor go with Shauna, Tierno and Trevor and meet Cassius, the manager of storage system and Emma, a young girl.
- Main article: Pokémon Adventures: Volume 3 (XY)
Cassius promises the children to take them to Cyllage City, where it is reported Grace, Y's mother, is located. Since Team Flare is after them, the group boards on a helicopter at the Battle Chateau. However, Y's schoolmates at the Sky Trainer Academy, who have been brainwashed, attack her with a dozen Vivillon. Fortunately, Y's Fletchy evolves and with help of X's Manectric, the group is defeated. However, Y's suit gets damaged and the helicopter crashes, separating Y from her friends. Y goes further on and overhears Malva and Celosia talking. With the help of Croaky (who evolved into Frogadier) Y follows Malva and Celosia, who reach Xerneas, who has turned into a form of a tree. They both leave and X, Tierno, Shauna and Trevor meet up with Y. X decides to follow Team Flare into their base, but not before he and Y rescue the villagers Team Flare had captured. Soon, Celosia arrives with the Vaniville Town's residents and seeing Grace, Y spoils the ambush. X, Y and their friends are trapped by a masked attacker with E on her helm, but help arrives as Korrina, Gurkinn and Diantha arrive. Korrina fights Celosia, Diantha battles Malva and X strikes at the masked attacker, using Gengar, Gurkinn has given to him. Gengar Mega Evolves and defeats Trevenant, inspiring Korrina to do the same to Celosia. While Diantha disappears with Malva, Korrina defeats Celosia. However, Celosia's Honedge attacks Korrina and her Key Stone is stolen.
- Main article: Pokémon Adventures: Volume 4 (XY)
While Y, Tierno and Shauna train with Gurkinn, Trevor visits the hospital with Cassius, where they meet up with the Gym Leaders - Grant, Valerie and Olympia - who would also fight against Team Flare. X, however, is depressed, as they failed to secure the Xerneas tree, as well as having Korrina's Key Stone stolen. X senses a message from Xerneas and gains courage to step up and battle Team Flare. Seeing Clemont's eyeglasses a Klefki gave to him, X moves to Geosenge Town, where he meets up with Emma. X enters Team Flare's lair and soon faces Lysandre, the boss of Team Flare, who wants to "seek out a more beautiful world", by using Xerneas. X sends his Pokémon to battle Lysandre. Meanwhile, X's friends meet up with the Gym Leaders (including Wulfric and Ramos) and encounter the Ultimate Weapon, which would destroy Kalos. While Y and the Gym Leaders suppress the weapon, Shauna, Trevor and Tierno go through the incinerator room, where they find Clemont, as well as Emma, who was talking to a giant man named AZ. After freeing AZ, the children move to the central chamber, where Lysandre had just defeated X. Trevor, being very angry, manages to blow away Lysandre and remove the key powering the Ultimate Weapon. Though they were late, the Ultimate Weapon only destroyed towns, but did not harm a single person. Xerneas bails them all out of the lair, where it chooses Y as its trainer. Just then, Malva appears, who had defeated Diantha and wants to do the same to the children. Since that would only mean an endless battle, the children and the Gym Leaders flee from the battle. Later on, they go to the Lost Hotel, where they discuss their strategies. After Y obtains a Mega Ring from Gurkinn (who saw her fit as a successor to Mega Evolution), she and X go to capture new Pokémon. Meanwhile, Diantha is rescued and taken away by Blue, who arrived to Kalos to assist them in solving the crisis between Xerneas and Yveltal.
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