Chuck Versus the Living Dead"Chuck Versus the Living Dead" is the 17th episode of the third season of Chuck. It was originally aired May 17, 2010. Chuck has another dream which he interprets as indicating Daniel Shaw may actually be alive. Tension mounts as he, Sarah, and Casey search for the truth surrounding Shaw's supposed death. Meanwhile, Stephen Bartowski (Scott Bakula) returns and discovers Chuck is still a spy, while Ellie continues to be manipulated by Justin.
The main plot of the episode is complex, with multiple story threads woven together. The episode begins at the residence of Chuck and Ellie's father, Stephen. He receives a secret message in the classified section of the newspaper from Ellie, telling him that she needs his address, and has to talk to him. He sends back a message saying that he will be in touch. Ellie calls Justin, and they arrange a meeting.
The ghost of Daniel ShawChuck discusses his dream about Shaw being alive (from the end of the previous episode) with Morgan over the phone, but when Sarah overhears he denies a problem and makes an excuse to see Morgan. Chuck meets Morgan at the Buy More, who becomes convinced that Shaw is alive and will target Team Bartowski. Chuck decides to keep this from Sarah due to a lack of solid evidence and also since she had a history with Shaw. Morgan convinces Chuck to let him stay in Castle until the threat is eliminated, but Sarah catches him there and gets the truth from Morgan, who is unable to withstand her questioning. Meanwhile, in the store, Chuck is going through Shaw's personal file when he spots his father entering. Stephen is likewise surprised to see Casey and Sarah, as he is unaware Chuck downloaded the Intersect 2.0. Chuck dismisses his concern by saying Casey works at the store now, and that he and Sarah are dating. At Castle, Sarah warns Chuck he should have been honest with her about Shaw, especially since his dreams could be the result of flashes while his brain is idle. Casey arrives and notes there has been no recent activity on any of Shaw's aliases, and that the best way to get to Shaw is by using Sarah's previous involvement as a starting point. As the team goes over their records, Chuck flashes on the building Shaw's penthouse is in, which contains a CIA safe. Sarah and Chuck decide to go investigate it.
Chuck and Sarah search the penthouse and locate the vault where the safe is located, but are unable to access it. Someone enters the apartment and Chuck and Sarah are forced to take cover in a closet. Through their infrared glasses, they watch a man open the safe and recover a briefcase, believing the man to be Shaw himself. Chuck's shoes squeak on the floorboards as the intruder prepares to leave, and he fires several shots into the closet before fleeing. Chuck and Sarah pursue him to the roof, where he attempts to escape by vaulting the gap between buildings. He does not make it all the way across and drops the briefcase. Chuck sends Sarah down to retrieve it while he attempts to pursue "Shaw." Chuck flashes, but is unable to clear the gap and is hanging from the edge when their quarry reveals himself to be Justin Sullivan, who tells them that Shaw is indeed dead. Before he can kill Chuck, Sarah opens fire on him from below and forces him to flee. Before he can fall, Stephen, who had followed Chuck, rescues him.
Back at Castle, the team determines the briefcase contained Shaw's last will and testament, which Sarah describes as containing everything about Shaw's work as a spy, to be opened by someone he trusts in the event of his death. The team concludes that if the Ring wanted its contents, then Shaw must indeed be dead.
However, a clip at the very end shows a figure placing his hand on a computer, the computer identifying him as Daniel Shaw, and an intersect uploading.
The IntersectStephen is unaware his son has uploaded the new Intersect and is still working as a spy when he arrives in Burbank, after having been summoned by Ellie. Despite Chuck's assurances at the Buy More that he no longer works for the CIA, Stephen is suspicious due to the continued presence of Casey and Sarah. He later confronts Chuck at home with the knowledge that his computer is still connected to the government's network, at which point Chuck claims to merely be working part-time as an analyst. After rescuing him from Shaw's apartment and returning home, Stephen forces Chuck to reveal that he possesses the new Intersect by throwing a knife at his son's face. Chuck successfully flashes and catches the knife, revealing the truth. Stephen tells Chuck that having the Intersect can have a negative effect on the brain and hastily rushes from the apartment.
Stephen returns to his own home and begins frantically working on a device concealed inside his watch. However, before he can complete his work, Ring operatives arrive and begin searching the cabin and attempt to beat the information on the device's whereabouts out of Stephen. Sarah was able to determine Stephen's whereabouts, and she and Chuck track him down. Chuck enters alone, not realizing that his father is in danger, and is captured himself. The Ring team successfully determines that Stephen has hidden the device they are after in his watch and prepare to kill the two with a propane explosion, but Chuck flashes on martial arts and attacks their captors. Sarah hears the commotion and comes after them as well. Between the three of them, the Ring agents are defeated and they return to Burbank.
Back at Chuck's apartment, Stephen reveals he was aware of the potential mental side-effects of the Intersect all along and spent a great deal of time attempting to develop a means of controlling the damage. He equates the effects to an overheating computer circuit, and tells Chuck that the Intersect functions by sending a large electrical pulse through the brain's neural pathways. It is these electrical impulses that can damage the brain, leading to emotional and mental instability or death. Stephen was able to successfully develop a device he calls the Governor, which manages the electrical impulses. He has confirmed that the Governor will also work for Intersect 2.0, and intends to create one for Chuck. He is also very proud of Chuck for using the Intersect like he did: to help people.
Meanwhile, Justin reveals the failure of his team to secure the Governor to another operative by phone, but orders him to proceed with their plans regardless. In a hidden facility, Daniel Shaw activates a computer terminal and is uploaded with the Ring's reconstructed Intersect.
EllieEllie is in Justin's office to report to Justin that she has made contact with her father and he will contact her again with further instructions. Justin warns her that John Casey is trouble, and gives her a set of speakers that will block all audio and visual reads from John Casey. Ellie returns to the apartment complex to discover her father has come directly to her rather than sending his location. When Ellie receives a call from Justin, she leaves to meet with him. Justin asks Ellie if she is prepared to carry out a little spy work for him in order to help her father, to which she agrees. When Stephen leaves after confronting Chuck about the Intersect, he bumps into Ellie, who attaches a GPS tracker to him.
Meanwhile, Chuck asks Casey to help him keep an eye on Ellie. He intercepts a message Ellie left for Justin on his phone and becomes suspicious that she may be having an affair. He tasks Morgan with quietly questioning Devon about their relationship, and it appears that he is indeed the perfect husband. With Morgan now assuming that the problem might be Ellie herself, Casey decides to search the apartment for more information. However, Ellie arrives home while he is there and is frightened when she realizes there is an intruder in the house. She calls Justin, who reveals that there is a gun hidden in the speaker he gave her. Ellie refuses to use the gun and instead hits Casey over the head with a frying pan before fleeing.
She returns to Justin's office for safety and asks about her family. Justin assures her that everything is fine and he will take care of Casey. Unbeknownst to Ellie, Justin locks her in the office.