Crystal first met Bonee when she was training to be a capture pro. It is there where an Arcanine was rampaging out of control due to an eye injury. Due to this, Crystal fell and broke her arms. Bonee and Monlee decided to intervene and attack the Arcanine to drive him away. After Crystal woke up they led her to the Arcanine, which she managed to calm down. Crystal added him to her team after the incident and Bonee used his bones to help her recover.
In Suddenly Suicune I, Bonee battled Suicune to try and help Crystal capture it. Crystal starts by having Bonee attack with Bonemerang, which is dodged by Suicune. Despite this Crystal reveals that it was part of her plan; The Bonemerang reverses direction, surprising Suicune, although it is dodged again. After failing to capture Suicune Crystal sends Bonee and Archy after it. Bonee rides on Archy and uses False Swipe while Archy tackles it. While it appears Suicune blocked it, it soon became obvious that a translucent wall between Suicune and Bonee was made. Bonee, alongside Crystal and Archy, attempt to keep the wall from closing but in the end Suicune closes it and escapes, breaking Bonee's bone in the process.
In You Need to Chill Out, Regice, Bonee was loaned to Emerald for his Battle Pyramid challenge against Brandon and his Regice. Regice began the battle by stomping with its leg, with Bonee barely managing to block with his bone. Bonee managed to block the attack for a long time but his bone eventually shattered under the pressure and Bonee was knocked out. Despite fainting Regice is quickly knocked out by Emerald's Sceptile, who was brought back thanks to a Revive.
In Skirting Around Surskit II, Bonee worked alongside Monlee by Emerald to help him capture Jirachi. Emerald has Monlee use Mach Punch to prevent Jirachi from moving by threatening to attack with his super fast punches. While Monlee kept Jirachi distracted, Bonee whipped out a pair of nunchaku made of bones. Bonee threw the nunchaku, which spun around Jirachi's body and bound it. However, due to interference from Guile Hideout, the capture fails.
Bonee is a gentle and caring Pokémon, as shown when he took care of Crystal after she broke her arms. He is a powerful Pokémon and one of Crystal's first choices when she needs a strong Pokémon. He shows no fear when entering battle and takes his opponents head on, even when facing strong Pokémon like Legendaries such as Suicune, Regice, and Jirachi.