The journey of Satoshi and his friends through the Kalos region continues! After Satoshi obtains his seventh gym badge, the group is moving toward the next town when Eureka discovers a mysterious Pokémon resting in her pochette. Soon given the name Puni-chan, it is one that even Satoshi and Serena's new Pokémon Zukan cannot identify. However, it quickly becomes apparent that Puni-chan is the target of a mysterious group clad in bright red suits known as Team Flare, aiming to capture the new Pokémon to further their agenda. But when Satoshi and the gang realize that the enigmatic organization has no intention of treating Puni-chan with any decency, they take a stand in opposition to Team Flare's plans, daring to fight back. With Gojika's predictions looming above them, Satoshi aims for his final gym badge while Serena contests for her last Princess Key in order to be able to compete at the TriPokalon Master Class. But as Team Flare begins to move in search of the mysterious Z, the stories of Pokemon XY and Pokemon XY: Mega Evolution cross paths as Satoshi and his friends, along with Team Rocket, get caught up in a scheme that could put Kalos in great danger.

Situated near the local zoo and owned by the charismatic polar bear Shirokuma, Shirokuma Cafe is a popular spot for animals and humans alike, allowing them to sit back and relax after a hard day of work. Whether it's a cold beverage or the latest item on his menu, Shirokuma finds joy in being able to serve his customers, often striking up conversations about various subjects. Together with the sarcastic Penguin and the clumsy Panda, they form an odd trio who get themselves caught up in all sorts of misadventures with their other friends such as Grizzly, a bar owner, and Sasako, a human who works at the cafe. From dealing with unrequited love, outdoor camping trips, karaoke sessions, and even the secret to brewing delicious coffee, there's always something bound to be happening in Shirokuma Cafe!

Satoshi and Pikachu have arrived in Lumiose City of the illustrious Kalos region to capture more Pokémon and continue their journey toward becoming the very best. Meanwhile, a genius inventor named Citron and his little sister Eureka wander the city when they run into Satoshi who quickly challenges them to a battle. However, they are soon caught up in a dangerous incident when Team Rocket, following Satoshi into Kalos, cause a Gaburias to rampage through the city. Far away in the quiet Vaniville Town, a young girl named Serena slogs through daily Sihorn riding practice at the behest of her mother, a professional Sihorn racer. After practice, she sees the events unfolding in Miare City on television where she recognizes a boy from her childhood. Having left a significant impact on her life, the sight of him stirs in her a desire to meet him again; and so, Serena sets off to Miare City, determined to find the boy from her past. Pokemon XY follows the group as they travel throughout Kalos in pursuit of their ambitions—Satoshi challenging Pokémon gyms, Citron learning from Satoshi, and Serena searching for what exactly her dream is. Along the way, they meet new friends, face new rivals, and continue to thwart Team Rocket's schemes, all the while discovering a little about the mysteries of mega evolution.

Prince Pietro is the half-human, half-dragon prince of the kingdom of Popolocrois. After the evil GamiGami tries (unsuccessfuly, as ever) to take over the Kingdom, a mysterious girl named Hyuu appears in the forest near Popolocrois Castle, which is the beginning of an adventure for Pietro, his witch friend Narcia, and all their friends. Set following the events of the first Popolocrois game.