Croaky was originally a starter Pokémon owned by Professor Sycamore. Croaky was first seen as a Froakie in An X-cuse to Come Out and Play, where he was given to Trevor alongside a Chespin and Fennekin in the hopes that X would pick one and leave his house and go on a journey. His attempt was interrupted by the appearance of the Legendary Pokémon Xerneas and Yveltal, which appeared in Vaniville Town and caused destruction as they fought each other. Although Trevor and his friends escaped, the case with Fennekin's Poké Ball and Pokédex was lost during the chaos.
In They Have a Flare for a Li'l Kanga-Napping, Tierno presented Froakie and Chespin to X and reveals that he, Trevor, and Shauna agreed that Froakie and Chespin should go to X and Y, as they are the best battlers of the group. X refuses both of them as he does not want them to be constantly targeted and attacked by their enemies, Team Flare, due to them being on his team. Later, Y finds the Team Flare scientists Aliana and Mable attempting to steal X's Li'l Kanga. When Mable attempts to have her Houndoom burn Y with its flames, Froakie saved Y with a wall of Frubbles. While X teamed up with Chespin to face Aliana's Diggersby, Froakie battled Mable's Houndoom. Eventually, X and Chespin managed to free X's friends from the room they were trapped in and pin Aliana and Mable to a tree, defeating them and giving X's group the chance to escape. Despite battling together, X still refused to let either Pokémon join him team.
In Fast-Thinking Froakie, Y is revealed to have decided to add Froakie to her team after having been inspired by X. While doing some Sky Trainer practice, an accident caused Y to fall to the ground, but she is saved by Froakie using his Frubbles to cushion the impact. As she thanks Froakie for saving her, Y decides to give it the nickname Croaky. Afterwards, Y decides to end her training for the day and goes in X's tent to change clothes in privacy. She is interrupted by an Electrike that steals her regular clothes and runs away. After Croaky uses his Frubbles to create makeshift top for Y, the group chases after the Electrike. With his speed and jumping skills, Croaky easily dodges Electrike's moves and takes back Y's clothes.
In Shooting Frogadier, Y and her friends were surrounded by a group of Sky Trainers controlled by Team Flare while in a helicopter piloted by Cassius. Y decided to leave the helicopter to confront the leading Sky Trainer. Y won the battle against her, but the helicopter began to break apart, forcing Cassius to make an emergency landing. One of the propeller blades broke off and hit Y in the head, causing her to be sent flying down towards Route 9. Her fall was broken once again by Croaky's Frubbles. As she traveled the route to try and get back to her friends, Y found Malva and Celosia talking about their next plan. Celosia, sensing Y's presence behind a boulder, used her Honedge to try and destroy the boulder, but Y and Croaky dodged in time. Just as Celosia took another swing, Croaky evolved into a Frogadier, grabbed Y, and leaped high into the air. He then took a piece of the boulder that was knocked into the air, covered it in a Frubble, and tossed it at a group of wild Rhyhorn, startling them into stampeding in front of Malva and Celosia. This convinced the two Team Flare members that there was not anyone else in the area. Afterward, Y began following Malva and Celosia to their next destination. Using his agility, Croaky stayed ahead of Y in the trees and alerted her when it was safe to move forward. With a trail of Frubbles he left behind, X and the others eventually managed to reach Y again.
In Malamar Traps, the group traveled to Pokémon Village to find Team Flare after they went into hiding. Upon arriving, the group was attacked by Xerosic, who used his Malamar to put everyone to sleep with Hypnosis. By evolving into a Greninja and blocking out the sound with his tongue, Croaky avoided falling asleep, allowing him to knock Malamar to the ground. When Malamar got back up, Croaky attempted to up his evasion while lowering Malamar's speed with Bubble, but due to a combination of Topsy-Turvy and Contrary, Croaky's attempts backfired, leaving him open to be put to sleep by Hypnosis.
Later, Croaky was woken up by Y so that she, Trevor, Tierno, and Shauna could go on ahead to the Pokémon Village. With his Smokescreen, Y and the others were kept from Xerosic's view, allowing them to sneak by him completely undetected. When Trevor faced off against Bryony all by himself, Y lent Croaky to him so that he would stand a chance against the Team Flare scientist in battle. With Croaky's ninja skills, Trevor kept himself hidden from Bryony, allowing Croaky and Floette to defeat Bryony and her Bisharp.