Beedrill first appeared in Golly, Golem!, battling in Giovanni's Gym battle against Red. After Giovanni's Golem defeated Red's Snor, he sent out Beedrill to corner Red with his stinger. Having Red trapped, Giovanni took the time to explain that he had read through each and every one of Red's decisions, ensuring that he would win. Asking Red to give up, Giovanni was surprised as Red released Aero from behind himself. Aero attacked with Hyper Beam and defeated Beedrill with a single hit.
In The Beedrill All and End All, Beedrill participated in Giovanni's battle against Lance at Cerise Island. Due to Lance surrounding himself and his Pokémon in an impenetrable bubble, Giovanni rolled Beedrill's Poké Ball underneath the main bubble. Beedrill came out of his ball and pierced the bubble with Twineedle, dropping Lance into the middle of a String Shot net made by Yellow's Kitty and entangling him. Beedrill then used his stinger to hold Lance at bay while Giovanni interrogated him. Despite this, Lance soon revealed that he had lured Giovanni into the center of the island on purpose in order to use his Earth Badge to activate his final plan.
At the end of the Ruby & Sapphire chapter, as revealed in a flashback in Omega Alpha Adventure 5, Blaise witnessed Giovanni taking thegems formed from the shattered Red and Blue Orbs. While Blaise intended to take them back, Giovanni sensed his presence and sent out Beedrill. He did not order him to attack however, as Blaise had retreated, having realized that he'd stand no chance against Giovanni.
Being Giovanni's first Pokémon, he and Beedrill have developed a strong bond that has lasted for years and he is often seen standing beside Giovanni. Despite not being Giovanni's specialty type, he prefers to use Beedrill, as he gives him a profound significance in his heart. He is fairly strong and is often used in Giovanni's battles, primary as a way to pin down his opponents.