Project Isis (also known as Operation Isis) was the CIA operation which saw Mary Bartowski abandon her own life to go deep undercover in Volkoff Industries, in order to get enough information to take the organization down. Mary was undercover for over twenty years.
It is unknown if the person in the CIA who arranged this knew that an intersect model had created Volkoff, as this was very sensitive information. It is unknown what information Mary was searching for originally, but towards the end she was known to be actively trying to steal Volkoff's Hydra Network.
It was presumably named for the Egyptian goddess of magic and death.