Steve J. Bartowski receives an encrypted message from his daughter Ellie saying she needs to get in touch with him. After receiving a reply, Ellie calls Justin to let him know she's made contact with her father. Chuck calls Morgan to tell him about his Shaw dream. Chuck believes Shaw is still alive, but he hasn't told Sarah yet. Morgan freaks out - they're in big danger! Chuck says it's up to them to take care of this. Fearful for his life, Morgan stays down in CASTLE.
Sarah catches Morgan down in CASTLE and uses her methods of persuasion to get information out of him. Morgan tells Chuck he told Sarah about Shaw. What's more surprising is that Chuck's father has arrived at Buy More. He doesn't know Chuck has downloaded the new At the Buy More. Steve notices Casey and Sarah are both there, which makes him think that not only is something fishy going on, but Chuck is still in the CIA. Chuck lies to his father and tells him he's no longer a spy.
Justin brings Ellie to a "CIA facility." As soon as they know where her father lives, he'll be safe. Down in CASTLE, Sarah tells Chuck he needs to be truthful with her and his father. Casey hasn't found any leads on Shaw. They should use Sarah to get to Shaw because of their intimate history together. The plan is to go over all the places that Sarah went with Shaw. Hopefully, Chuck will FLASH on something. Although this makes Chuck a bit uncomfortable, he knows he has to go along with it.
Casey asks Sarah what she and Shaw did in Washington D.C. After spending some romantic time together, Sarah was given a massage and taken to Tiffany's, where she received new earrings. Finally, when Sarah mentions Shaw's loft downtown, Chuck FLASHES. Shaw used this penthouse loft to construct a TR-15 safe. Whatever's he's hiding in there, it could lead the team to Shaw's whereabouts.
Outside Buy More, Jeffster performs "Love Hurts." They're begged to stop by passers-by. Big Mike offers to help the band by becoming their manager. Jeff wants in, but Lester doesn't, so the band breaks up. Lester takes the "ster" out of Jeffster.
Steve makes a surprise visit to Ellie at her apartment. Chuck assigns Casey to watch over Ellie to make sure she's safe. Chuck joins Ellie and his father for dinner, but winds up taking off for a mission with Sarah. When Ellie gets a call from Justin, she bails on her father too. Ellie goes to meet Justin alone, still under the impression that Casey's a threat.
Steve's convinced that Chuck's a spy and that he's lying to him. He sees all the evidence around the apartment. Chuck continues to lie, claiming he only does analysis work for the CIA, nothing dangerous. Later that night, Chuck and Sarah climb into Shaw's downtown penthouse loft. Ellie waits alone for Justin, while Casey eavesdrops - could Ellie be cheating on Awesome?
At the penthouse, Sarah finds the safe using thermal glasses. She and Chuck are just about to crack it when someone enters, whom they assume to be Shaw. They hide in the closet while he opens the safe and removes a briefcase. When Chuck's sneaker squeaks against the ground, the man shoots into the closet. Chuck and Sarah chase after him, but he jumps across the roof to another building and drops the briefcase.
Sarah runs to get the briefcase while Chuck skill FLASHES on the Long Jump. Chuck jumps to the other building, but misses the landing, and winds up dangling by his fingertips. He looks up to see Justin stepping on his fingers, with news that Shaw's dead. Sarah shoots from the ground below to save Chuck, but he's losing his grip. Another set of footsteps approach, but this time, instead of another bad guy, it's Chuck's father, Steve, who saves him.
Chuck brings his father down to CASTLE, but continues to lie about being an active spy. Casey and Sarah open the briefcase, which holds Shaw's lockbox containing a spy's last will and testament. Everything Shaw knows about the CIA is probably in this document and The Ring wants it, which means that Shaw really is dead. Sarah reads Shaw's letter, which confirms that not only is Shaw dead, but Chuck was wrong.
Steve doesn't think the mission's ever over. He understands the importance of the lockbox. This is why he doesn't want his family to have any part of the spy life. Back at Justin's office, Ellie learns she must start doing some real spy work to protect her father. Meanwhile at Buy More, Big Mike tries to manage Jeff, and Lester misses his band mate.
Casey tells Morgan that Shaw's dead and Chuck was wrong. Casey wants to know if Ellie would ever cheat on Awesome and lets Morgan listen to part of Ellie's conversation with Justin. Morgan wants to help Awesome, so he talks to him, asking about his daily life with Ellie. By the end of their conversation, Morgan seems like he's in love with Awesome. There's nothing this guy can do wrong.
At the apartment, Steve confronts Chuck about still having the Intersect. Chuck keeps lying about this until Steve throws a knife at his head. Chuck skill FLASHES on knife defense to catch it, shocked that his father threw a knife at his face. Steve tells Chuck that the Intersect has a negative affect on the brain. Steve says he has to leave because he can't stay and watch his son die. Steve takes off and Ellie gives him a hug goodbye; little does he know that Ellie has just placed a tracer on his jacket.
Chuck tells Sarah about his fight with his father. Sarah thinks Chuck should talk to him; she knows where he lives. In the meantime, Steve takes something from his watch and places it in the computer. Suddenly, Steve's surrounded by Ring agents. The leader knows Steve has an Intersect and wants to know what's keeping him alive. Just then Chuck knocks on the door (as Sarah waits in the car) and is also taken hostage by the agents.
The Ring wants to know where something called the "Governor" is. The agents release gas into Steve's apartment and things look bleak for the father and son team, until Chuck proves to his father that he can help people with the new Intersect. Chuck skill FLASHES on Tonfa Fighting and takes out the Ring agents. Sarah hears a scuffle inside and comes to help. When Steve joins in the fight, the three of them are able to defeat the team of Ring agents.
Steve isn't sure how The Ring found his cabin, but he knows the agents came for the Governor, something that governs the Intersect, kind of like a pacemaker for the heart. Steve's gotten close to fixing it for the first Intersect, and he can make something work for the Intersect 2.0. Steve accepts Chuck's spy life and Chuck thanks his father.
Big Mike convinces Lester to rejoin Jeffster, and tells him about his old days in Earth Wind and Fire, when Big Mike used to be "Rain." He hands Lester his old jumpsuit and tells him to wear it with pride. Morgan tells Casey that Ellie's apartment should be empty and to go check it out - something's not right. Casey places a bug on Ellie's phone, but she arrives home early and hears him in the house. Ellie calls Justin, who tells her where he hid a gun. Ellie uses a pan to knock Casey out and Justin arrives just in time to take her away.
Later that night, Sarah gives Chuck her spy will, because if anything happens to her, she wants Chuck to have it. Justin takes Ellie back to the "CIA facility" and unknowingly locks her in the room. Chuck begins to write his spy will as Casey regains consciousness. And somewhere far away, Justin makes a phone call to Shaw, who's still very much alive. The team can't wait anymore. After hanging up the phone, Shaw downloads the Intersect 2.0.