The Hydra was Alexei Volkoff's main network, enabling him to secretly monitor and control all of his operatives and his arms deals anywhere in the world. Mary Bartowski spent most of her time working at Volkoff Industries learning about Hydra, as her original orders were solely to find it. It has possibly been used to monitor Mary's actions in "Chuck Versus the Aisle of Terror", which would have explained her drastic measures in shooting and exposing Chuck as a CIA agent during a supposed weapons transaction, where Chuck was under the guise of Charles Carmichael.