Z2 first appeared in From A to Z! in its 50% Forme, where it was attacked by Mable, a group of Team Flare Grunts, and their Pokémon in Terminus Cave. Z2 was able to overpower them and send them flying with ease using Land's Wrath, and escaped its pursuers. It was later seen outside Terminus Cave, watching the sunrise.
It reappeared in Meeting at Terminus Cave! and A Cellular Connection!, as a Zygarde Core, where it was contacted by Squishy. During one of their conversations, Z2 tried to convince Squishy to cut contact with humans, claiming them to be destructors of order. Squishy, however, disagreed with it, wanting to continue observing humans.
In An Explosive Operation!, Z2 was cornered by Mable, Aliana, and a trio of Grunts under their command. When it tried to escape via camouflage, it was hit by Team Flare's special ray gun, stunning it and disabling its cloaking. To overcome this, Z2 entered 10% Forme and used Extreme Speed to fend off the scientists' Weavile and Druddigon, and make its escape. After reverting to its Core Forme, Z2 ran into Team Rocket, who had recently set their sights on Squishy. Discovering that there were two Zygarde Cores, the trio tried to capture Z2 themselves, but were stopped by Team Flare. Jessie, James, and Meowth protected Z2 from Team Flare's ray gun, which was then destroyed by Inkay. Jessie then used Gourgeist's Seed Bomb to escape with the Zygarde Core.
Exhausted from their escape, Team Rocket let Z2 recover by allowing it to absorb sunlight. Soon after recovering, however, they were once again found by Team Flare. Although the trio fought hard, they were eventually defeated. Left with little options, Z2 transformed into its 50% Forme and fought back with Dragon Pulse and Land's Wrath, overpowering Team Flare's Pokémon. Before Z2 could finish off Team Flare, it was stopped by a Flamethrower from Alain's Charizard. Alain and his Mega Charizard X then battled against Z2, covering for Mable and Aliana. After taking a Dragon Claw Z2 managed to blast Charizard into a rock with Extreme Speed. It was then struck by Dragon Claw again, but Z2 quickly retaliated with Land's Wrath, dealing serious damage to Charizard. Despite having gained the upperhand, it was eventually surrounded by the two scientists, who proceeded to stun it with full-power blasts from their ray guns and sapping its strength, causing it to revert back to its Core Forme. After blasting away Team Rocket, Z2 was secured by Mable, who deemed the operation a success. Z2 was later seen at Lysandre Labs, glaring at Lysandre.
Following these events, Z2 was seen several times, being observed and experimented on by Lysandre and Xerosic. It appeared again in Seeing the Forest for the Trees!, where it was listening to Squishy talk about Ash and his Greninja.
Z2 under Lysandre's control
In Kalos League Passion with a Certain Flare!, Z2 was moved into Lumiose Gym with several Zygarde Cells in preparation for the climax of Team Flare's plans. Team Flare's scheme was put into action in Down to the Fiery Finish!, where Z2 was placed under influence of Team Flare by Xerosic's Mega Evolution energy weapon. After reaching the summit of Prism Tower, it transformed into its 50% Forme and unleashed massive roots through the city and the Lumiose Conference stadium, interrupting the ending ceremony. In the next episode, Z2 continued to destroy Lumiose City. Even when Squishy confronted it atop Prism Tower, Z2 did not respond and launched a Dragon Pulse at Squishy which overpowered the latter's Dragon Pulse and knocked it down from the tower. After Squishy transformed into its 50% Forme, Z2 jumped down to battle it. During their battle in Coming Apart at the Dreams!, Z2 took some harsh hits from Squishy, but was eventually able to constrict Squishy with its giant roots, allowing Xerosic to hit Squishy with the Mega Evolution energy weapon. With Squishy being controlled as well, both Zygarde continued their rampage.
Z2 was finally freed from Team Flare's control in the the following episode, after Clemont and Clembot managed to destroy the machine. Later, it reunited with Squishy and after listening to it talking about the things it had experienced during its travels with Bonnie, Z2 reluctantly began to trust humans. It later accompanied the group to the Giant Rock. After witnessing how hard everyone was fighting to protect Kalos and after a brief conversation with Squishy, Z2 finally came to understanding that not all human beings are evil and decides to believe in them just like Squishy does. Z2 and Squishy stepped in and combined into their Complete Forme and used Core Enforcer to destroy the Giant Rock, causing Lysandre to vanish. Both Zygarde then said goodbye to everyone and disappeared with each other.
It appeared in a flashback in Battling With a Clean Slate!.
Z2 reappeared in Facing the Needs of the Many! alongside Squishy, where the two rescued Team Rocket from getting hit by a root. Ash and his friends were later brought to Z2 by Squishy, and the two Zygarde Cores explained that they had been weeding out negative energy left over from the Team Flare crisis, energy of which was spreading throughout Kalos in the form of the same roots that destroyed parts of Lumiose City. However, tracking down the source of the negative energy proved to be a difficult task for them to accomplish. Having witnessed Greninja's ability to locate the negative energy within the roots, Z2 and Squishy asked Greninja to lend them its strength to protect Kalos, which Ash agreed on. Z2 then left with Squishy and Greninja, bidding farewell to Ash and his friends
In Till We Compete Again!, Z2 appeared alongside Squishy as both oversaw Ash's Greninja destroying a root that was attacking the Kalos region.