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The episode opens directly after the last one left off, with Chuck and Sarah at his dad's, Steve Bartowski (Scott Bakula). Chuck eventually convinces his dad to come back for Ellie's wedding and when they arrive back home, Ellie initially doesn't want anything to do with him. Chuck eventually convinces her to give him a chance while they leave poor Awesome alone in the room with him. Crazy Steve rambles on abou thow is old college friend, Roark stole all his ideas. Chuck sees a Roark NextExpo information card and flashes. Beckman soon reeals to him that their new OS their launching may have a huge virus. Chuck is going to have to get a job there... using his real name and Stanford degree.
Jeff and Lester convince Big Mike to let them attend the NextExpo and they head off to camp out there. They see Chuck walking out having gotten a job there, and they immediately phone Morgan about the "traitor." At dinner that night, Morgan mentions the new job in front of Steve who is hurt his son took a job with Roark. At his first day of work, Chuck has to keep on eye on Roark during the announcement of their new OS as Casey and Sarah try and get to the source code. When they aren't going to make it in time, Chuck steals the remote control that launches the new OS from Roark's hands. After being chased around they end up catching him and Roark launches the software.
Chuck comes home that night and ends up looking at the Intersect schematics again and realizes they line up perfectly with Roark's office.. they have an Intersect! He tells Sarah who doesn't believe him. He heads to Castle where Casey tries to stop him. He tells Casey about the Intersect and ends up having to shoot him with a tranq gun (three times!) to be able to go. Chuck sneaks into Roark where he ends up running into his dad with four security guards! He shoots them all and soon our favorite Fulcrum agent, Vincent walks in, and says it's nice to see you both. Steve uses a computer on his wrist to close the security door on Vincent and Chuck quickly realizes his father is Orion!!
They get to a secured door, and Steve tells Chuck to flash on the password.. it's the last thing he'll ever flash on again. He manages to and they get into a room with Intersect 2.0. They sit down to remove the Intersect from Chuck's head when Roark comes in with his men. He orders them to kill Chuck, but Steve makes a deal that will save Chuck's life... he'll fix the Intersect for them. Sarah and Casey show up as the door opens for Chuck to leave and they have to drag him away from his dad.
At the end of the episode, Ellie, who has been heart broken the whole episode, comes home to a pancake dinner (the last meal promised to her by her dad) made by Awesome. He promises to never leave her, but he lets her know her father split down. Chuck tells her not to count their father out just yet. We cut over to Steve working on Intersect 2.0.