When we last saw the bunch-of-bees-forming-a-humanoid called Swarm, The Champions had defeated him (her?) by hurling the queen out to the ocean, causing the bees to disperse. leaving behind the skeleton of the host body.
The remains were brought to Empire State University, where bees found it and became Swarm again.
Spider-Man tracks Swarm (after being stung a LOT) to a giant hive and beats up the giant queen.
He also admits that bees are scary because, yeah, they are. And he uses science, adding bug repellent to his web fluid.