With Chuck, Sarah, Morgan, and Casey all working under Carmichael Industries as freelance spies, Morgan has to learn to handle his Intersect 2.0 whereas Chuck has to rely on his spy skills after his Intersect was removed.

After the death of his dad, Chuck enlists the help of Sarah, Morgan and Casey to help free his mother Mary, from the clutches of black market arms dealing organization, Volkoff Industries.

After downloading the Intersect 2.0, Chuck finally chooses to be a spy, to Sarah's chagrin. Six months later after failing spy school, he is fired from the CIA and also lost the love of his life. CIA Agent Daniel Shaw takes over Team Bartowski to aid Chuck's journey into becoming a spy.