Peeko was with Mr. Briney, who caught Ruby with a net, as he was drifting on the sea. Once Ruby woke up, he was greeted by Mr. Briney, who explained Peeko found him. As a Crawdaunt emerged from the sea, Peeko used Quick Attack, but Crawdaunt's Shell Armor negated the damage. Crawdaunt, however, slammed Peeko to the ground. After Ruby and his Skitty, Kiki, subdued Crawdaunt, Ruby bandaged Peeko's injuries and even gave the Wingull some makeup. After arriving to Dewford Town, Ruby and Sapphire faced each other. This made Mr. Briney and Peeko worried how much they can insult each other.
Peeko was with Mr. Briney, who became a captain of a ship.
Mr. Briney and Peeko, as well as Mr. Stone and Drake, stood at the ship, where Mr. Stone got a picture from Steven, which showed murals from Granite Cave. After reuniting with Sapphire, Emerald, Steven and Ultima, the group sailed towards Sea Mauville. Due to Zinnia's assault, Mr. Briney had Peeko attack Team Aqua and Magma grunts. Peeko used Soak on Zinnia's Goodra to help Ruby battle her.
Due to Primal Kyogre's power, the ship and everyone on it, including Peeko, were drowned in a whirlpool.
|Quick Attack||Stick This in Your Craw, Crawdaunt II|
|Soak||Omega Alpha Adventure 9|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.
- In one of the chapters, Peeko's name was misprinted as Pepper.
- ^ RS010: Blowing Past Nosepass I
- ^ RS012: Stick This in Your Craw, Crawdaunt I
- ^ RS013: Stick This in Your Craw, Crawdaunt II
- ^ RS014: Guile from Mawile
- ^ RS087: It All Ends Now VIII
- ^ FRLG027: Mewtwo and Mew Too
- ^ EM015: Sneaky Like Shedinja I
- ^ ORAS002: Omega Alpha Adventure 1
- ^ ORAS005: Omega Alpha Adventure 4
- ^ ORAS006: Omega Alpha Adventure 5
- ^ ORAS009: Omega Alpha Adventure 8
- ^ ORAS010: Omega Alpha Adventure 9
- ^ ORAS013: Omega Alpha Adventure 12