A brilliant but eccentric scientist invents teleporter pods that accidentally merge him with a housefly, turning him into a human-fly hybrid. As he deteriorates and becomes more monstrous, he seeks help from his ex-girlfriend while struggling with his changing identity.

The Fly II follows the story of Martin Brundle, the son of Seth Brundle who was transformed into a human-fly hybrid. Martin, who inherits his father's telepathic abilities and accelerated aging, becomes a victim of his own DNA. With the help of his love interest and a sympathetic scientist, Martin tries to escape the clutches of his father's former employer who seeks to exploit his abilities.