Sarah’s got the Intersect in her brain, which she uses to sneak herself and Casey aboard the bullet train that Quinn is currently riding with Chuck. Chuck is briefly mad about Sarah uploading the Intersect, but then they discuss how cool it is to flash. And then they do the only thing they can do: have sex on the insanely fake-looking bullet train (it’s got pristine blue and yellow walls with white leather seats and bed pods that appear to be from the Shatner-era Star Trek TV series). Then they draw pictures of them as a happy little family with a baby and that stupid white picket fence. Don’t they know those pickets are a pain? That you can get splinters and you have to replace them because they rot?
So Casey’s stuck watching Quinn, and it’s fine until Quinn reveals that he’s had a team kidnap Alex from the Buy More (where she was buying pizza Combos for Morgan, who is stuck down in Castle getting tested by Ellie and Awesome to find a way to stop the Intersect from ruining Sarah’s memory). Sarah is able to stop Quinn by using the Intersect, but it turns out she can’t control it and has flashed 40 times in two days. Perhaps she shouldn’t have wasted it learning to read Japanese in order to open up one of those bed pods when there were other ways to figure that out without taxing the in-brain computer. But Casey’s still concerned about his daughter, and dispatches Morgan and Awesome to stop the Flu Bus (the not at all clever or subtle disguise by Quinn’s henchmen), but they end up trapped on the bus as well. And then, in the most anticlimactic scene ever involving a flamethrower, Jeff and Lester come in to save the day. Casey had to clue them in on what’s been happening, and they mostly just object to all the brain memory wiping — something that people should care more about, given that saving memories is what they are all desperately trying to do for Sarah.
Speaking of, Chuck’s building an Intersect-suppressant device, which should probably be marketed in pill form given how often the CIA needs to use it now, to help Sarah. But Quinn’s found his way back on to the speeding bullet train, and despite their best efforts, Casey and Chuck are stuck in one car, while Quinn and Sarah are in a caboose that gets detached. We don’t get to see them trying to get off that car before it crashes or any fun things you normally see in movies, instead we skip to some mysterious amount of days later in a warehouse with some ugly little hologram flashcards that he uses to force Sarah to flash. More than a little on the nose and annoying there, show. And she subsequently tries to draw Chuck to their location by using a tracking beacon. Now, how did they get back from Japan so fast? Could Quinn not find an abandoned warehouse somewhere in Asia? Has Sarah been gone hours? Days? Weeks? Months? There’s no real indication. But by the time Chuck gets to the warehouse, Sarah’s already gone. Quinn’s successfully erased her memory, placed her back in her old CIA hotel room, posed as her handler and told her to kill Chuck Bartowski.