Morgan grabs Casey in the Buy More and tells him he talked to Awesome and, if Awesome would have him, he'd let him. In other words: It pains him to say it, but if there's a problem here, it's on Ellie's side. Morgan asks why he's doing this, and Casey says he gave Chuck his word Ellie would be safe. Uh, actually, you promised to shadow her, which you're not doing so great at. Morgan tells Casey that Ellie's at work and Awesome's volunteering at the animal shelter (but of course he is), so the apartment's empty. Casey heads over to check it out. He goes upstairs and then Ellie comes home, on the phone with Justin. She tells him he can come there because Awesome won't be home so it's totally safe. Justin's on his way, but Ellie hears footsteps upstairs. She asks how close he is, and Justin tells her to go to the speaker and open it. She pulls out a gun, but says she can't. Justin tells her that someone's in her house and could hurt her or her family. She puts down the phone and holds the gun as Casey sneaks down the stairs. Ellie's hiding behind a column in the room when Casey comes up. She bashes him over the head with a frying pan, then runs out, into Justin's arms. He tells her she's safe and to come with him. Casey's knocked out on the floor.
When Chuck gets ready for bed, he sees Sarah sitting seriously on the end of the bed and asks what's wrong. She tells him she's been thinking about what his dad said about the life they've chosen not being safe and he's right. So she's giving him her spy will. He asks why, and she says it's her, everything she knows, so if anything happens to her she wants him to have it. He says nothing's going to happen to her; she's not going anywhere; and neither is he. Ellie, however, might be a different story, because Justin tells her everything's good and she's saved and protected everyone and has been brave. He tells her he'll be back soon, and then leaves and locks her in the room. She doesn't know it yet, though.
Chuck's on a computer, writing his own spy will. "My name is Chuck Bartowski, and if you're reading this, that means I'm already dead. I don't know what will end up killing me. But I've chosen to be a spy and there are consequences to that." Casey wakes up on the floor and touches his face, which must be in some serious pain. "It may be my emotions that end up doing me in." Sarah sleeps in Chuck's bed. "Or a slip-up trying to protect my friends." Morgan's asleep in his own bed. "Or my family." Ellie's still sitting and waiting for Justin. "Who never wanted me to be a part of this." Bakula's working on the Governor. Justin makes a call, saying "This needs to happen now. No more waiting." Because his team was captured. In an Intersect room, we see the back of someone as he hangs up and puts his hand on the Intersect pad. It lights up and does that thing that made Chuck the Intersect, as the guy holds his hand there. We never see his face, but when it finishes up, we see the handprint monitor, which says the download was confirmed to Daniel Shaw. I'm guessing we only saw him from behind because they couldn't get him for this episode, only the next one, but it seems really weird. "Or it could be the thing I never saw coming. But I know. It's coming."