At Castle, Sarah pulls a tranq out of Casey, who wakes up. She asks where Chuck is. He thinks for a second and then says, "In a world of pain." Chuck's telling his dad he can't believe he invented the Intersect. Bakula says he only invented the really cool stuff. Bakula can understand how this might complicate a few things, as he continues to lead Chuck using his arm, which apparently comes equipped with GPS. Chuck's all, "Complicate?!" since he saw him explode in a helicopter. Bakula sees how he could have given Chuck that impression, but he's had to die quite a few times. It's one of the perils of being Orion. It's not what he wanted, but when he saw what the government was going to do with the Intersect, he had to run. And then he knew the government wouldn't be the only ones looking for him, so he had to stay away from Ellie and Chuck. He opens a door and leads Chuck into a computer-filled room.
Chuck asks if he was protecting Chuck and Ellie. Bakula says he knew he'd have to spend his life hiding from the Intersect, but never dreamed it would find Chuck. He imagines it's a curse having those secrets trapped in his head. That's why he came back, and let Sarah find him. It's his fault. Fulcrum's after both of them now. As he says this, Chuck flashes back to (different than flashing on, of course) Orion typing, "Because I'm Orion." Then on Orion's computer face. Then on he and Sarah driving up to the trailer. Then on his dad laying the flier out strategically. Then on the Roark folder. Chuck says Bakula wanted him to flash on the schematics, and wanted Chuck to break in, so asks why he didn't just tell him who he was and what he wanted. Bakula wonders if he would have trusted him after ten years. Chuck wouldn't have. They're at the door pad that stumped Sarah and Casey. Bakula tells Chuck to flash on the code. Chuck says it doesn't work like that; unless it's in there, he can't do it. Bakula says he can. He would know, since he designed the computer. He tells Chuck to flash for the very last time. Chuck looks at it intensely, and flashes on the code. He punches it in and Bakula awesomely says, "Aces, Charles," and they go inside the room.
The room is very sterile and white with blue lights. So it looks vaguely like the Fortress of Solitude. There's a tiny, little, bright, glowy box spinning inside a cylinder, which Bakula says is the Intersect. Chuck can't believe that's it, but Bakula casually says "2.0. The greatest thing I ever created. Except you and your sister." Bakula has to make some software modifications, so he makes transparent computer screens come up, and starts typing. He tells Chuck that, in theory, the Intersect should be able to take out information. He's going to flash some images at Chuck that will cancel out the ones in his brain. Chuck's all, "Wait. Are you saying you're going to overwrite my brain?" Bakula says that's a good way of putting it. Bakula's ready, so Chuck reminds him he needs glasses. Bakula wishes Chuck luck and pushes the button.