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Beedrill was encountered at Vermilion Forest. It was part of a swarm of Beedrill that attacked Go when he caught Kakuna. When the others were trapped by Pikachu's Electroweb, Go caught the lone Beedrill that wasn't hit, assuming it was the strongest. Beedrill and the rest of the Kanto Bug-type Pokémon Go caught were brought back to the Sakuragi Institute where Professor Sakuragi kept them in storage for Go.
It was used in SS014 to battle against a giant Golurk, only to be defeated in 1 hit.
In SS015, it was used to locate Cubone's missing bone.
At the Sakuragi Institute