The Zygarde Core first appeared in Mega Evolution Special IV, where Mairin's Chespin, Chespie, recovered it from an experiment being done in the Lysandre Labs. Although the Core escaped, Chespie fell into a coma. At some point after escaping Team Flare, it found its way to a bag on a stump, which the tired Order Pokémon decided to sleep in. This bag turned out to belong to Bonnie, who became quickly enamored with the cute Pokémon. It attempted to escape to no avail. Ash and Serena attempted to scan it to learn what it was, but neither Pokédex recognized it. Bonnie then nicknamed it Squishy in the absence of a species name and decided to take care of it despite Clemont pointing out that they knew nothing about this Pokémon.
Squishy was quickly separated from the group after Sawyer's Grovyle chased a group of Dodrio through the forest the group was in. The group, together with Sawyer, soon caught up to it, only to find it being captured by Team Flare Scientist Celosia and a group of Team Flare Grunts. Celosia referred to Squishy as theirs, but as her harsh treatment made Ash and his friends skeptical of this claim, they went on to save Squishy. The five and their Pokémon were able to escape with Squishy none the worse for its ordeal.
After escaping, Squishy was introduced to the rest of the group's Pokémon. During dinner, the group was confused that Squishy was refusing to eat, but understood when it basked in the setting sun and absorbed sunlight. Soon after, it went berserk upon seeing Terminus Cave on Serena's Town Map and attacked the device, which the group interpreted to mean it wanted to go there.
That night, it detected through its cells that Celosia and the Team Flare Grunts were still searching for it, so it woke the group up. It was attacked by the Grunts again, but Ash and Sawyer, still unconvinced that Squishy belonged to them, defended it while Serena, Clemont, and Bonnie carried it away from Celosia's group. However, it was separated from the three after Bonnie fell while crossing a river, leading to it being cornered by Bryony. Out of desperation, it absorbed surrounding cells to transform into its 10% Forme, allowing it to use Land's Wrath to force Bryony and her subordinates to retreat. Although this exhausted it, it absorbed light to heal itself. It was then found by Bonnie who promised she wouldn't let it go again. Seeing that Ash and his friends meant no harm, Squishy began to trust them and decided to travel with them.
In Love Strikes! Eevee, Yikes!, Squishy was shown to Professor Sycamore who was informed that neither of the two Pokédexes recognized it. Sycamore then went on to say that it could be a new Pokémon. While resting in Bonnie's bag, Dedenne wanted it to make space for it so that Dedenne could rest. Serena then decided that she would make an extension for Squishy to rest. While Serena was stitching Bonnie's bag, Squishy went to rest on a rock nearby and absorbed sunlight for itself to re-energize. When the stitching was done, both Squishy and Dedenne were happy as they could now rest in Bonnie's bag. Later, Squishy got kidnapped by Team Rocket, along with Serena's Eevee, Clemont's Bunnelby, and Dedenne. They managed to escape, but were quickly found again. When Bunnelby and Dedenne got defeated by Gourgeist, Squishy prepared to change its form and attack them, but stopped when Ash and the group arrived.
In Dream a Little Dream from Me!, after the gang viewed the Litleonid meteor shower, Squishy separated from the rest to sleep in a nearby tree. A Darkrai also happened to nestle in that same tree, and started showing Squishy a nightmare, pulling Ash's Pikachu and Team Rocket's Meowth into its dream. In the dream, the group's Pokémon were either in their evolved or pre-evolved form and could speak human language, while the humans spoke like Pokémon. Pikachu and Meowth met up with Squishy, who was getting chased by a flaming ghost. Squishy showed them a glimpse of its true strength, before attempting to escape to its home so it could access this power. After the defeat of the flaming ghost, it was woken from its dream by Clemont's (failed) invention, and promptly found by Ash and his friends.
When Ash and his friends finally arrived at Terminus Cave in Meeting at Terminus Cave!, Squishy separated from the group and continued alone to an underground lake in the cave. When it arrived at the lake, it got detected by a sensor placed by Team Flare. In the waters, it began meditating and contacted Z2. When the group arrived at the lake, their conversation ended and Squishy camouflaged itself. Then Team Flare entered Terminus Cave who, after spotting Squishy using their special scopes, managed to injure Squishy by shooting it with their specialized laser guns. During a hard fought battle between Ash and his friends and Team Flare, Squishy transformed to its 10% Forme and proceeded to defeat Team Flare's Pokémon. Celosia and Bryony then sent out their Manectric and Liepard to try and stop Squishy, but they were stopped in their tracks by Ash's Greninja and Pikachu, giving Squishy the chance to escape. After Team Flare had retreated, Squishy was seen hiding behind a tree, watching the group.
Squishy was continuously seen watching the group in the following episode. It also contacted Z2 again, who tried to convince Squishy to cut contact with humans. Squishy, however, disagreed with Z2 and wanted to continue observing humans. Later, when Bonnie was trying to get the medicine for Clemont's Bunnelby, who got injured earlier, Squishy helped Bonnie to reach it. At the end of the episode, Squishy returned to Bonnie's bag and had a tearful reunion with her.
In An Explosive Operation!, Squishy sensed something was wrong with Z2, as it was getting chased by Team Flare, greatly worrying it. At the end of the episode, Squishy felt incredibly upset after realizing Z2 had been captured by Team Flare and vowed that it would come to rescue it.
In Seeing the Forest for the Trees!, Squishy used its cells to find a safe hiding spot for the group after they got stuck in a snowstorm looking for Ash. It later went out to look for Ash after his friends started getting really worried. While in its 10% Forme, it eventually met up with Greninja and told it of Ash's location, which it had tracked using its cells. At the end of the episode, when Ash and Greninja had returned, Squishy sent a message to Z2, telling it that Ash and Greninja truly embodied the unity between people and Pokémon.
In Volcanion and the Mechanical Marvel, Squishy turned into its 10% Forme to protect Pikachu from a Mega Banette's Will-O-Wisp by using Dragon Pulse to counter the move. Soon after, it aided Pikachu by allowing him to ride on its leash, to get in close to a Mega Aggron and hit it with Iron Tail. Later Squishy was seen fighting with a Mega Glalie, before turning into its Complete Forme from afar and firing a Dragon Pulse to counter the laser that Alva had shot from his airship at the Nebel Plateau. Neither Bonnie nor the rest saw Squishy turn into its Complete Forme. It then reverted to its Core Forme before rejoining the group.
During the Lumiose Conference, Squishy typically hid in Bonnie's bag, but in Finals Not for the Faint-Hearted!, it stayed out to watch Ash and Alain compete in the finals. During the awards ceremony, the stadium was attacked by Team Flare and Z2, now under Team Flare's control. Squishy sensed Z2 going berserk, and left Bonnie and the others in the confusion. In A Towering Takeover!, Squishy transformed into its 10% Forme to make its way to Lumiose Gym, while trying to reach out to Z2 telepathically. Z2, however, did not respond. As the sun began to set, Squishy climbed Prism Tower to confront Z2, but its Dragon Pulse was overpowered by Z2's own Dragon Pulse, sending it off the edge of the tower and causing it to revert to its original form. With no other choice, Squishy called for more Zygarde Cells and transformed into its 50% Forme to match Z2. In the process, Ash and his friends realized that Squishy is in fact a Zygarde like the one attacking the city. Squishy continued its battle against Z2 in Coming Apart at the Dreams!, where it used its Extreme Speed to dodge Z2's roots and slam into it with full force. Squishy, however, was eventually subdued by the roots, allowing Xerosic to hit it with the Mega Evolution energy-powered beam, controlling Squishy. Now being controlled by Team Flare as well, it proceeded to take part in Z2's destruction of Lumiose City.
While continuing its destruction in the the next episode, Squishy was eventually confronted by Bonnie and Blaziken Mask. Bonnie's attempts to calm it down didn't work, however, and Squishy attacked her with its roots, slamming Blaziken Mask into a wall, who stepped in to protect Bonnie. As Squishy neared Bonnie and prepared to attack her with Dragon Pulse, Bonnie made one last attempt to save Squishy by singing Puni-chan's Song. The song managed to get through to Squishy, freeing it from Team Flare's control. After reverting back to its Core form and reuniting with Bonnie, Squishy left to find Z2, who had been freed from Team Flare's control as well.
Upon finding Z2 in the following episode, it tried to explain to the skeptical Core that humans and Pokémon are worthy to be trusted, telling it about the things it had experienced during its travels with Bonnie. It was then brought along with Bonnie when she and the others chased and tried to stop the advancing Giant Rock. In Forming a More Perfect Union!, while watching everyone fight the Giant Rock, Squishy once again talked with Z2 and convinced it that humans, along with Pokémon, were worthy to be trusted and saved. After gaining the trust of the other Core, both of them joined hands and transformed into their Complete Forme. With this Forme, they managed to stop Lysandre, destroying the Giant Rock and thus returning Kalos' environment back to normal. After this, it had to properly rest and left the group, but not before expressing its gratitude towards Bonnie and her companions for protecting it all of this time and showing it that both humans and Pokémon may have the determination to never give up.
It reappeared in a flashback in Battling With a Clean Slate!.
In Facing the Needs of the Many!, Squishy and Z2 rescued Team Rocket from getting hit by a root. Squishy later appeared before Ash and his friends, protecting them from another root. After having a tearful reunion with Bonnie, it told Ash's Greninja to follow it, and led the group to Z2. There, Squishy explained that it and Z2 had been weeding out the 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, it asked Greninja to lend them its strength to protect Kalos, which Ash agreed on. Before Squishy left with Z2 and Greninja, Bonnie promised that she would come back for it when she was old enough to be a Trainer.
In the following episode, Squishy and Z2 both oversaw Ash's Greninja destroying a root that was attacking the Kalos region.