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 A Photoshoot and the Abandoned Thrifty Megamart, 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 met Sun and asked him to collect the remaining Cells and Cores, offering him one hundred thousand yen for each of the forty Cores and Cells remaining. Sun accepted the job and received the Zygarde Cube in order to store any Cells and Cores that he finds.
Six months later, Zygarde formed itself into its 10% Forme from the Cells Sun had gathered in the Zygarde Cube. It used this form to keep Sun safe from the wild Nihilego at the Ultra Deep Sea. The Order Pokémon was unable to keep this form for long and reverted back to Cells immediately after.
In Meeting the Ultra Recon Squad, Zygarde again formed 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 arrived in Ultra Megalopolis with Zossie and Lunala. After landing, the Ultra Beast Stakataka appeared in hopes of fighting the weakened Necrozma. 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.
In PASM31, when Necrozma opened an Ultra Wormhole back to Alola, the Cells quickly left Sun and traveled to the Aether Base's Reassembly Unit, where it formed itself into its Complete Forme. The Order Pokémon then traveled to the summit of Mount Lanakila, where it reunited with Sun. In PASM35, Zygarde confronted Necrozma, who used energy absorbed from Dulse to turn into Ultra Necrozma. Despite its best efforts to keep Necrozma from fleeing and absorbing Alola's light, Zygarde was blown apart by Necrozma's Photon Geyser, reverting it back into Cells. Zygarde quickly reformed itself into its 50% Forme and used Camouflage to blend in with its surroundings. When Necrozma was about to finish off Sun and Solgaleo, Zygarde attacked the Prism Pokémon.
Necrozma quickly dropped Zygarde to half of its stamina and it reformed back into its Complete Forme. Shortly after, Moon arrived and gave Solgaleo a Max Revive while her Decidueye stopped Necrozma's movements with Spirit Shackle. With Necrozma's movements stopped, Zygarde teamed up with Solgaleo and Lunala and defeated the Prism Pokémon.