He starts a ticking bomb and puts it in Sarah's lap. Then he thanks Chuck for leading them here; he couldn't have done it without him. Chuck shakes his head at Frost and tells her he believed in her. Volkoff tells him not to take it personally; there's no point in going to the grave with regrets. Frost says she's ready, then leans forward to check Sarah's ties. But she really slips a razor into Sarah's hand and tells her to protect Chuck. She and Volkoff leave, and Chuck tells Sarah that she was right about Frost, and he was stupid to believe her. He tries to flash, but can't. His mom did something to him with that device (I don't think it was getting rid of the Intersect, however; I think it's something new he's yet to discover). They get free and Chuck worries about his dad's files, but Sarah says there's no time. They make it outside as the place goes up in flames. Outside, he tells Sarah he can't flash anymore and now all of his father's research, everything he ever created, it's all gone.
Except not quite. Because, see, he created Chuck and Ellie. And this one other thing he left to Eleanor. Cut to Awesome and Ellie finding the car, in perfect condition. She can't believe it's been here this whole time -- and with the top down! And a letter inside for Ellie. She opens it, and it reads: "Eleanor, If you're reading this, then it means I'm not with you anymore. And I know you'll be okay. I only wish I could have been the father you deserved. ... But our family had a lot of secrets. Secrets I kept from you because you were so young, because I didn't want to hurt you. I know you're a grown woman now, but no matter what, you'll always be my little girl, curled up on the middle seat of this car. This is my final gift to you, Eleanor. And I'm giving it to you now for a reason. I trust you'll know what to do. I love you always. Dad." As she drives the car away, the camera moves under the hood, where there's a green glowy light.