Harkov was an agent protecting President Boris Vorshevsky and part of the FSO under the command of Leonid Pudovkin. He held off the Ultranationalist terrorists that attempted to hijack the President's plane while it was en route to Hamburg. Andrei is blindsided at the beginning of the attack, and is tasked with rescuing the president's daughter. Before the plane crash Pudovkin stayed with the President while Harkov fought with another agent who then falls out of the plane leaving only Harkov and Pudovkin to survive until the end. As Andrei struggled to not fall from the plane, the remnants of an engine slams into his section, knocking him unconscious. After the plane crash landed, he and Pudovkin attempted to retrieve the President. As Pudovkin, Vorshevsky, and Vasili get ready to board the helicopter, Harkov opens the door only to find Vladimir Makarov holding him at gunpoint and then is shot. Pudovkin pulls out his gun but is shot before he is given a chance to kill Makarov. As Makarov gets Vorshevsky onto the helicopter, Harkov reaches for Pudovkin's pistol but is spotted and executed by Makarov.
He is one of the four playable characters to meet Vladimir Makarov face-to-face.
When Harkov died, the screen turns black unlike other playable characters (such as PFC. Allen and Sgt. Jackson) where the screen turns slowly to white; this is similar to Yasir Al-Fulani's and Farid's execution.
In the intro of the mission "Turbulence", an obscured photo can be seen with the words "Inside Man? Andrei Harkov."