Chuck, Stephen Bartowski, Sarah and Casey discover that Shaw is still alive. Chuck, Sarah, and Casey then go on a mission to try and expose that Shaw is still alive and working for the Ring. While Stephen Bartowski goes back into hiding.
Ellie is brought to the CIA Base by her handler and Devon, convinced by Morgan thinks Ellie is having an Affair.
Meanwhile Chuck, Sarah and Casey are led to the CIA Base thinking it's a Ring base. Chuck discovers Ellie there and hit's her handler. Ellie learns that Chuck is working with the CIA.
Chuck, Sarah and Case are brought before the heads of CIA, NSA who came from Washington to evaluate Operation Bartowski aka The Intersect Project.
General Beckman tries to convince half of Washington that Operation Bartowski has been successful. However Shaw, who has an intersect in his head too, convinces Washington that Chuck is insane and seems to prove it as Chuck tries to convince everyone that Shaw has his own intersect, he then throws a knife at Shaw expecting him to catch it but ends up stabbing him. This convinces Washington that Chuck is crazy and he get thrown in a holding Cell.
Chuck,s dad returns to help Chuck escape while Shaw tricks Sarah and Casey to turn on the CIA. Sarah is captured while Casey escapes to finds his estranged daughter, Alex, and convinces her that he really is her Father. Casey is then captured and held in custody with Sarah at the CIA Base.
With Ellie's help Chuck and his dad find and infiltrate the Ring Base. Shaw rushes over to the Ring Base and confronts Chuck and his Dad. Earlier Stephen Bartowski had made a special watch called the Governor which governs the intersect so Chuck doesn't go crazy. Now that chuck has the Governor he is ready to fight Shaw. Although unexpectedly Shaw shoots Chuck's Dad in the Chest and he dies in Chuck's arms. Before he died he said to Chuck "You're Special Son". Ellie witnessed the shooting from a distance.
Shaw then takes Chuck into custody with Sarah and Casey.
Beckman, while scrambling to destroy important files knowing the Ring has infiltrated the CIA and will arrest her any minute, rings the castle and finds Morgan and Devon there. Beckman says it's up to them to save Chuck, Sarah, Casey and her.
Morgan and Devon talk to Ellie. Devon is relieved Ellie is not cheating and then Morgan and Devon fill Ellie in about Chuck and the CIA and the Ring.
Chuck, Sarah and Casey are on their way to a detention facility in an armoured truck. Chuck who is very devastated at the loss of his Father loses all hope and thinks no one is left to save them.
The episode ends with Ellie following the armoured truck while on the phone to Devon, who is sitting with Morgan in Casey car.