In An Egg Scramble!, Dawn battled Lyra in the Johto Festival and defeated her. As a prize, Dawn was given an Egg, which was soon abducted by Team Rocket. While it was in Team Rocket's possession, it showed signs of hatching. When Dawn finally got it back, it hatched right in front of her eyes, revealing it to be a Cyndaquil.
In Last Call — First Round!, Cyndaquil was used in the Performance Stage of the Sinnoh Grand Festival along with Buneary. Their performance started with Buneary using Ice Beam to create a large frozen path resembling a roller coaster. Cyndaquil proceeded with Flame Wheel, rolling over the path and melting a trench for Buneary to slide on. After that, Buneary charged an Ice Beam and Cyndaquil used Smokescreen in order to cloak themselves above a large frozen spike. When the smoke was blown away, Buneary was seen inside a Poké Ball made of ice with Cyndaquil standing on top, impressing the Contest Judges and securing Dawn a place among the Coordinators advancing to the Contest Battles.
As a Cyndaquil, it developed a strong bond with Dawn from the moment it hatched from its Egg. Prior to entering its first Pokémon Contest, it grew interested in watching Dawn train her other Pokémon, often showing Dawn its own variations of the moves that she was practicing with them, and sulked when it was not chosen to compete.
Dawn's Piplup appears to be jealous over the attention that it gets, though this may be attributed to the fact that Cyndaquil wasn't very responsive to Piplup at first. Piplup often attacks it and it in turn fights back, causing frequent squabbles between the two. They seem to be trying to compete for superiority over the other. These fights have stopped ever since Cyndaquil evolved.
It has a tendency to flare up its back when it's happy or when it's showing affection, and Dawn usually ends up getting burned in the process.
Description: Used in the Tag Battle with Khoury and Lyra and Ash and Dawn, It starts off with Cyndaquil running ahead and using Flame Wheel and while Cyndaquil somersaults into the Flame Wheel, Ash's Monferno uses Flamethrower towards Cyndaquil causing more flames to gather and a speed boost towards the target.
Description: A combination which was created by Mamoswine and Cyndaquil when they were training with Dawn. It involves Cyndaquil being trapped by Mamoswine's Ice Shard while utilizing Flame Wheel. It was perfected in the battle against Ursula in Playing the Performance Encore!. Dawn calls it "Flame Ice".
Description: Mamoswine uses the Swallowing Ice Shard Technique to create the Ice Armor. Cyndaquil then uses Swift in a circle around Mamoswine. Then Cyndaquil makes the flame on its back split into two. Mamoswine then uses Take Down while Cyndaquil is on the top part of the Ice Armor.
Description: Cyndaquil developed this while training with Dawn in Twinleaf Town. Cyndaquil would perform it by firing a ring of Swift into the air, then jumping into the center and charging Flame Wheel, causing the two moves to mix.
Description: Piplup jump ons top of Cyndaquil and forms Bubble Beam into a circle and Cyndaquil uses Swift in the middle of the circle. It is unknown what Dawn was going to do with this, as Johanna destroyed it with her Glameow and Umbreon in a matter of seconds.
Description: Piplup would surround Cyndaquil's Flame Wheel with a Whirlpool, which created the effect of a sphere of water with flames inside. Dawn attempted to use this during her second battle against her mother, however the combination failed throwing both Piplup and Cyndaquil to the ground.
Quilava is the only Pokémon belonging to a main character to have evolved in a side story episode.
Quilava is the only Pokémon Dawn owns that is not a Generation IV Pokémon.