Deep Red is a thrilling story about a secretive young woman who hires disillusioned private eye Joe Keyes to locate her husband, Warren Rickman. He successfully finds him, but soon realizes that they are being followed by two strange, seemingly bulletproof, yet highly inflammable goons disguised as milkmen. These goons attack them, assassinate Rickman, and frame Joe for murder.
With the help of his friend, Det. Sgt. Eldon James, Joe locates Mrs. Rickman and her little daughter Gracie, who are under the protection of his ex, Monica Quik. It is revealed that Gracie is infected with revolutionary futuristic nanobots known as "Deep Red", which possess incredible healing abilities that scientist Dr. Thomas Newmeyer wants for himself at any cost. The "milkmen" are revealed to be working for him.
Joe agrees to help the girls, despite the case bringing back painful memories of his failed attempt to save the family of Eldon's partner, Mack Waters. Waters holds a serious grudge against Joe and is determined to see him dead.