To find out if Chuck's nightmares about Shaw are real, Casey and Sarah help Chuck try to locate Shaw. After going over the guy's information, Chuck flashes on a safe in his penthouse, and Chuck and Sarah head there. Meanwhile, Ellie brings Stephen Bartowski (Scott Bakula) back for Justin and he begins to suspect Chuck is back to being a spy, but Chuck lies to him for fearing of admitting he put the Intersect 2.0 back in his head after fighting so hard to remove 1.0.
At the penthouse, Chuck and Sarah find the safe, but someone arrives at the door! As with any Chuck spy sequence, the action turns into a shootout and they chase who they think is Shaw to the roof. While falling short on a rooftop jump and clinging to the edge, Chuck learns the masked guy he's been chasing is Ellie's Justin. Sarah rescues from below with a gun shot and Stephen from above with a hand!
Stephen now obviously knows his son is a spy and heads back home, because he refuses to stay there "and watch his son die." As per Justin's orders, Ellie places a tracking device on his back. Meanwhile, Sarah uses old-fashioned spy work to locate Stephen and the two head over to talk to him.
Chuck arrives at the crazy shack where Stephen has already been ambushed by the Ring. After fighting off the bad guys, Stephen tells Chuck they were coming for the "governor," a watch that can regulate the Intersect from damaging the brain.
Ellie knocks out Casey, who's been assigned to shadow her the episode, and ends up leaving with Justin.
The episode ends with Justin calling Shaw, telling him it needs to happen now. Shaw loads the Intersect into his brain! OMG. Alive and badder than ever.
Oh and there was a Jeffster subplot where Big Mike became their manager. They split, but Big Mike brings them back together.