Zygarde was first alluded to in Rhyhorn Charges, by Blue when he contemplates if the power of "Z" could stop Xerneas and Yveltal. It was later shown in silhouette and mentioned by name by Diantha when she and Blue were conversing on the crisis happening in Kalos. Diantha planned to seek out Zygarde, with the help of Korrina and Gurkinn, which Blue agreed to help with. It first physically appeared in Hawlucha Attack, behind the Sundial of Anistar City, where it startled a few Spritzee and disappeared afterwards.
Later, it is revealed from Xerosic's flashback that when AZ escaped from Team Flare’s HQ during the clash between Xerneas and Yveltal, he mentioned that their plan will fail because of the Overseer of Kalos will appear when the order is disrupted, calling the Overseer as Z. Xerosic figures out that he was referring to Zygarde. With little information of it, he sent Essentia out to find and capture it. Meanwhile, at Anistar City, as Essentia loses control of Xerneas, Zygarde appears and Essentia decides that it is more important to focus on the Order Pokémon. She uses her Trevenant to trap it with tree roots. Zygarde attempted to retaliate by summoning the forces of nature and absorbing them into its body. Doing so left it completely defenseless, allowing Essentia to easily capture it and escape. At that moment Blue and Diantha approached, witnessing Essentia successfully capturing Zygarde. Blue then explains to the others about Z's key role in helping to win the fight against Team Flare.
Zygarde was later placed in Emma's PC Box. After Lysandre used a special device to completely control Essentia, it was retrieved and started battling. At the Pokémon Village, Lysandre planned to use Zygarde to battle against X, Blue, and Blaine. As it battled Mewtwo, X had Marisso smash Essentia's helmet in the hopes that it may sever Lysandre's connection to Zygarde.
Lysandre continues ordering Emma to have Zygarde attack. Emma does so and uses it to defeat Blaine and Mewtwo. Cassius soon arrives and tells Emma that she doesn't need to work with Team Flare and has his Gourgeist destroy Lysandre's controller, breaking his connection to Zygarde. Now freed, Emma attempts to have Zygarde attack Lysandre, only for his Gyarados to attack her. He takes Zygarde's Poké Ball, thus making it under his command, using it to attack with another Land's Wrath, causing everyone to be sent flying. After Lysandre loses his Mega Ring, X returns with his entire team sent out. Though he is impressed by his feat of Mega Evolving his entire team, Lysandre is unfazed by X's attempt and sends Zygarde to battle X's Mega-Evolved team. It continues to fight X's team as Emma notices green blobs breaking off from its body, remembering that Zygarde absorb it into its body while in Anistar. At that moment, as Xerneas and Yveltal are returning into their dormant forms, Zygarde begins 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.
After the battle, Zygarde noticed high amounts of energy in Alola coming from the Ultra Wormholes and Ultra Beasts and left for Alola. In Epilogue, after the battle had ended, Blue and Blaine visited Professor Sycamore and told 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.
Six months later, a Zygarde Core is shown in Po Town. In PASM16, Dexio and Sina arrive at Ula'ula Island. Since being sent to Alola, the duo had successfully gathered sixty percent of Zygarde's Cells and Cores. Shortly after they find Sun and ask him to collect the remaining Cells and Cores, offering him one hundred thousand yen for each of the forty Cores and Cells remaining. Sun accepts the job and Dexio gives Sun the Zygarde Cube in order to store any Cells and Cores that he finds. Sun later begins collecting the remaining Cores and Cells.
Six months later, Zygarde forms itself into its 10% Forme from the Cells Sun had gathered in the Zygarde Cube. It uses this form to protect Sun from being attacked by a group of Nihilego at the Ultra Deep Sea. The Order Pokémon was unable to keep this form for long and reverted back to Cells immediately after.
Later, Zygarde again forms itself into its 10% Forme to attack Zossie's Poipole after Dollar and Moon's Dartrix were defeated by its poison. Zygarde caused major damage to the Poison Pin Pokémon but was also taken out by Poipole's poison, reverting it back to its Cells.
Soon after, Sun and Moon arrive in Ultra Megalopolis with Zossie and Lunala. After landing, an Ultra Beast Stakataka appeared in hopes of fighting the weakened Necrozma. Zossie took Sun and Moon to the Megalo Tower, where they met Soliera, another Ultra Recon Squad member. Soliera lured Stakataka to the tower as she wanted to test the bonds between people and Pokémon in order to find a way to return light to the Ultra Megalopolis. By disguising itself as a building, Stakataka hid itself from view, allowing it to easily capture Sun. Moon and Lunala fought to rescue Sun, but were unable to use their full strength without risking Sun's safety. After noticing Stakataka's many eyes, Sun had Moon shoot the Zygarde Cube with an arrow, releasing Zygarde Cells everywhere. The Cells stuck to Stakataka, blinding it and preventing it from dodging Lunala's next attack.
Personality and characteristics
Zygarde is known as Kalos's "Overseer" (Japanese: 監視者 Watcher), monitoring the ecosystem and takes action once it falls into disarray. It will attack anyone in its way and is neither a friend nor foe to Xerneas or Yveltal. Zygarde is able to summon the forces of nature, which appear in the form of green blobs, and absorb them into its body. It is very protective of Sun, being quick to defend him from other Pokémon.