In their car, running, Bakula presents Chuck with his Governor, which is all finished and ready to save his brain. Chuck puts it on and tells his dad that he feels better. Chuck's phone rings; it's Morgan. Bakula tells him that a cell isn't off the grid, but Chuck says he didn't get to say goodbye to Morgan. He answers and starts telling Morgan he has to go off the grid and won't be around for a while. Morgan says that Agent Superman got Casey and Sarah, and even General Redhead. Chuck's like, "What?!" But his dad grabs his phone and throws it out the window. He says that Agent Superman kidnapped them all to lure Chuck and get the Governor. Bakula says that Chuck can't ask him to put his own son in jeopardy. Chuck asks Bakula why he came back? To protect Ellie and him. Because he knows that he couldn't live with himself if something happened to someone that he loves. Bakula tells him that if they do this, they have to be smart and not think emotionally, but they can do this: "We're Bartowskis."
Chuck shows up at Ellie's. She drops and breaks her tea cup and tells him she thought the CIA still had him. He says he wishes he had time to explain. Ellie, fed up, tells him that it takes as long to say that as to tell him what's going on. He tells her they need her help. She asks who "we" is: the government? He says no, but Bakula walks in and says they actually mean the two of them. He says that they have the answers they need right now. She leads them to the bench where she used to meet Justin, and ask her to walk them through it. She points them to the door that Justin would go into when he left her. It's another subway door. Chuck and Bakula tell her to stay right here, on the bench, and run if they're not back in 20 minutes. She keeps Bakula behind and tells him she needs to hear him say that there's a reason he left them. He tells her it's a long story and she deserves to hear it, but they have to take care of this first. He tells her this is the last time he'll walk away from her, and hugs her. He says he loves her, and then he and Chuck head inside the door.