X & Y
Zygarde debuts in the X & Y chapter. It was first mentioned by Blue, who aimed to find it in order to stop the endless battle between Xerneas and Yveltal. It appeared in person at Anistar City, where it was sought after by Essentia, who aimed to capture it for Team Flare. When X and Y battle Essentia in order to retrieve Y's stolen Xerxer, Zygarde appeared before them and attacked before Essentia manages to successfully capture it.
Zygarde is later used by Essentia to battle against X Blue and Blaine. After Emma is freed from Lysandre's control, she was about to order Zygarde to attack him but he manages to take its Poké Ball making it fully under his control. Zygarde is later used to fight against X's Mega Evolved team, but as the battle progresses Emma notices green blobs falling off of it. At that moment, Xerneas and Yveltal are returning into their dormant forms, causing it to disintegrate, and X hits it with a combined attack from his team. This resulted in Zygarde exploding into millions of green blobs, and Lysandre begins to fall. Soon after the battle ended, Blue and Blaine visited Sycamore and mentioned to him about seeing a little green silhouette after Zygarde disintegrated into the blobs. Sycamore reveals to them that such green silhouettes have been spotted in a far away region as well, and sends Dexio and Sina to investigate them in Alola.
Sun & Moon