Megaree first appeared in Murkrow Row. He was originally a Chikorita owned by Professor Elm alongside a Cyndaquil and a Totodile. After Cyndaquil and Totodile were taken by Gold and Silver, respectively, Chikorita was left alone in Professor Elm's laboratory.
In Three Cheers for Chikorita, Chikorita learns about Crystal, a Trainer who specializes in capturing Pokémon. Professor Elm initially intended to give Chikorita to Crystal, but she already had a full team and had no intention of adding any more permanent team members. Upon learning this, Chikorita gets angry and runs away to find Crystal.
He finds Crystal attempting to capture a wild Victreebel on Route 30. Just as Crystal attempts to attack the Victreebel with Archy, Chikorita steps in the way, forcing Crystal to stop the attack. Victreebel takes this opportunity to use Chikorita as a shield, preventing Crystal from attacking. After having Chumee prevent Victreebel from escaping with Mean Look, Crystal captures both Chikorita and Victreebel. Crystal attempts to transfer Chikorita over to Professor Oak, but Chikorita stops her and reveals he wishes to join her team. Crystal, believing Chikorita to be too weak to join what would be a dangerous journey to capture Pokémon, refuses to let him join her team. When Chikorita still chooses to join her, Crystal sends out Monlee to battle against him. Monlee easily blocks Chikorita's Razor Leaf and even shatters the ground in front of Chikorita with a Mega Punch. Despite being outmatched, Chikorita stands his ground and refuses to run away. Impressed by his bravery, Crystal allows Chikorita to join her team and names him "Megaree" for his mega guts. As Megaree would take his spot on Crystal's team, Chumee gave Megaree her star pendant so that he would match the rest of Crystal's Pokémon.
In Suddenly Suicune I, Megaree participated alongside the rest of Cyrstal's team in her attempt to capture Suicune.
In Lively Larvitar, Megaree battled a wild Larvitar that was responsible for Archy's eye injury in the past. Although Larvitar proved to be a powerful opponent, it was eventually defeated when Megaree evolved into a Bayleef, allowing Crystal to capture it.
In Lively Lugia II, Megaree is happily reunited with Exbo and Totodile, who have since evolved into Quilava and Croconaw, respectively. Together, the three fend off a wild Lugia at the Whirl Islands. When Lugia attempts to crush them under its weight, Megaree, Exbo, and Croconaw work together to hold Lugia up. The strain of this causes Megaree, Exbo, and Croconaw to evolve into Meganium, Typhlosion, and Feraligatr, respectively. Though they succeed in saving their Trainers, Lugia eventually escapes.
In The Last Battle XIV, Megaree is used alongside the other starters to try and stop the Masked Man's attempt to capture Celebi.
In The Final Battle VIII, Megaree helped destroy Guile Hideout's fake Kyogre monster. Having learned Frenzy Plant from Ultima, Megaree teamed up with Red's Saur and Emerald's Sceptile to unleash a triple Frenzy Plant at the fake Kyogre. Together, along with a triple Blast Burn, a triple Hydro Cannon, and a triple Volt Tackle from the other starters, the fake Kyogre is ultimately destroyed.
In All About Arceus V, Megaree, Exbo, and Silver's Feraligatr attacked the incomplete forms of Dialga, Palkia, and Giratina created by Arceus. Through a combination of the ultimate attacks, the three Legendary Pokémon are stopped, though this only delays their completion.