Prior to the start of the series, Giovanni caught Beedrill when he was a Weedle at Viridian Forest when he was a young Pokémon Trainer. Sometime after this he evolved into a Kakuna and then into Beedrill. Since then, Giovanni has used Beedrill as a reliable partner in many situations as the boss of Team Rocket. He notes that while he prefers to use Pokémon of his specialty type, his origins have given him a profound significance in his heart.
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 the gems 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.
In It Takes Patience, Knowledge and a Really Quick Beedrill, Beedrill helped Giovanni capture Organism No. 2. Using his Agility Beedrill quickly backed Organism No. 2 into a corner, causing its Delta Shield to quickly lose energy. Thanks to this, Giovanni's Aggron was able to break the shield with Brick Break, allowing Giovanni to capture it.
In Omega Alpha Adventure 17, Beedrill appeared alongside Giovanni aboard his airship. In Omega Alpha Adventure 20, Beedrill was revealed to be able to Mega Evolve. Giovanni used his Mega Evolution to reveal that the meteoroid headed for Hoenn may be housing a Pokémon inside of it, since Mega Evolution can only be used in battle with another Pokémon. In Omega Alpha Adventure 21, Beedrill assisted in stopping the Grand Meteor Delta.