At the Tokyo train station, Chuck walks with Quinn who's pointing a gun at his ribs. They board the Shinkansen Japanese bullet train. Chuck asks Quinn what their destination is but Quinn refuses to say. Chuck tells Quinn he's not sure what he expects of him since he can't fix the Intersect. Quinn tells Chuck he doesn't believe him. Plus he thinks Chuck wasn't properly "incentivized" with a gun to his head. Chuck is confused because Quinn doesn't have the Intersect in his possession. Quinn tells him Sarah and Casey delivered the Intersect glasses to his men. And the bad news is that Sarah and Casey are both dead.
Two coffins in the train's cargo car unseal and creak open. Sarah and Casey pull off oxygen masks and sit up. They're not dead after all! Sarah says they're right on schedule because things go smoothly with the Intersect. Casey is skeptical because of what happened to Morgan when he was carrying the Intersect. She reminds him they were able to take out Quinn's henchmen in short order and were able to send him phony communiques. Casey wonders how Chuck will react to her having the Intersect. Sarah says she's going to wait for the right time to tell him.
Back at Castle, Morgan is hooked up to electrode contacts while Ellie, Awesome and Alex look on. Ellie is trying to determine if the flawed Intersect was actually triggered by a natural occurrence in Morgan's brain - all in the hope of preventing the same thing from happening to Sarah. Morgan would prefer to be in Tokyo helping the team. Meanwhile back in Tokyo, Chuck is in handcuffs and sitting in a private compartment on the train. Chuck secretly slides off his wedding ring revealing that it's actually made of two parts. He connects the two parts and makes a handcuff key. He unlocks his handcuffs and tries to get off the train but one of Quinn's men catches him.
Quinn's men cuff Chuck to the seat and one of them is about to throw out his ring/secret key when a ceiling vent pops open and smashes the henchman on the head. Sarah drops from the vent and lands on Chuck's lap. Chuck is relieved to see her alive and asks Sarah how she got there. She tells him, "That's actually a funny story." The other henchmen attack and she flashes the Intersect before taking them out. Impressed by the display, Chuck wonders if she's doing "Strip Kick." She confirms only that she's "upgraded" her fighting technique. She tells him they have to run. Sarah talks to Casey via earpiece and asks him how the cargo door is coming along. He tells her it's sealed and he's working on it; but they may have missed their window to get off the train before it departs. She tells him not to worry; she'll figure something out.
Chuck and Sarah arrive at the train's cargo area and find Casey failing at his attempts to override the cargo door. Just then, Quinn arrives with gun drawn. He wonders how they were able to send fake messages to him. "I'll applaud you later," he says and tells them not to move. Sarah flashes the Intersect and quickly grabs the nearest thing, an umbrella, and hits Quinn in the chest, sending him backwards into one of the coffins. Just as Casey is about to slam the lid on him, Quinn yells, "You don't want to do that, I know more than you think!" Casey tells Chuck he won't be able to get out because the digital locks are inside and he'll never figure out the combination.
Still needing to get off the train, Sarah goes to the middle of the car and pulls open a hatch in the floor revealing the ground rushing by in a blur. She tells Chuck and Casey there's a coupling under the train that leads to an exhaust intake. She remembered it from an earlier flash. Casey nixes the idea, telling Sarah that maneuver may be easy for her but they're going to have to wait until the next train station. Chuck can't believe he heard Sarah say flash so he asks what she meant. Sarah finally admits to him, "Chuck, honey. I have the Intersect. Surprise?"
While Chuck tries to get his head around the fact that his wife has the Intersect, Casey and Sarah try to figure out a way to get off the train. They conclude they have to sit tight until they reach the next stop, which is Yamashiro station. They'll contact Beckman and have her waiting there with an Intersect suppression device along with Japanese intelligence to take control of Quinn. Still distracted by the Sarah Intersect revelation, Chuck asks if it's the same Intersect Morgan downloaded. Sarah confirms that it is but wants to talk about it after they figure out how to get off the train.
At Castle, Morgan is now in a hospital gown with electrodes covering his head. He's annoyed, but Alex tries to calm him down. Ellie and Awesome are at a computer monitor studying an MRI of Morgan's head. Ellie can't find any evidence of long-term effects from the Intersect but still can't figure out what triggered the memory loss. Ellie and Awesome hypothesize that since Morgan had the Intersect for an entire month before the amnesia and during that month he hardly flashed at all, the amount of time he flashed probably had something to do with it. Morgan is still agitated he's not in Tokyo helping the team, so Alex offers to get him some food. He asks for pizza combos, and she goes upstairs to the Buy More.
Chuck and Sarah are in a private compartment on the train. She's finished explaining how and why she has the Intersect. He understands but is worried what happened to Morgan will happen to her. Sarah tells him Ellie is working on figuring out how to fix the problem. Aside from that, it'll be gone from her head in an hour and a half when they get to the station and meet Beckman with the suppression device. After a brief moment of silence between them, they simultaneously blurt out how cool the Intersect is. Sarah admits that even though she's been a spy for so many years, she's never felt so powerful.
Chuck asks Sarah if she's ready to give all that away. No more guns, no bullets. She tells him she's done living in constant danger and ready to retire and start a family. Chuck points out they still have a little time before they reach Yamashiro and starting a family isn't just something you dive into. Sarah agrees they'll need practice. He goes to the car's control panel but can't read the Japanese. Sarah flashes and presses a button that opens up a cozy sleeping capsule. She zips open her spy suit to reveal she's wearing red lingerie. Chuck exclaims, "Domo arigato, Mr. Roboto!" and they head for the capsule.
At the Buy More, Big Mike spots two nurses handing out flu shot flyers. Mike doesn't know anything about it and asks who authorized it. They tell him it was Morgan. Mike is annoyed because "nobody tells nobody nothing." He then spots Lester sneaking around the microwaves and catches him trying to explode an avocado in one of the units. Mike chastises Lester telling him it's time for him to grow up. With Mike gone, Jeff comes up to Lester having overheard the conversation. Lester doesn't want to talk about it. Jeff brings up the fact they're having the same dreams. It's like someone wiped their memories clean. They need to figure out what's going on. Lester thinks he's just better at blowing up avocados.
Meanwhile Alex passes Jeff and Lester on the way to grab Morgan's pizza combos. One of the flu nurses comes up to her and asks if she's had her flu shot. Alex tells him she already has but the nurse pulls out a gun and shoves it into her ribs saying, "Well come get another or I'll kill you right here." Alex is stunned but complies. He leads her out of the Buy More. Jeff and Lester pop up from behind an adjacent aisle. They witnessed the whole thing. Jeff tells Lester in his previous state of impairment he wouldn't have noticed or cared. But now, they have to find the truth even if they "have to face mortal danger." Back on the train, Casey is guarding Quinn who's still in the casket. Quinn asks Casey to open the casket but Casey refuses. Quinn then confirms with Casey that Alex McHugh is his daughter. His interest immediately piqued, Casey opens the casket. Quinn gives Casey his cell phone. Alex is on the line and confirms to Casey that Quinn's men have captured her.
In the private compartment, Sarah and Chuck are post-coital and lying in the capsule bed. Chuck is holding a Japanese magazine and drawing over an advertisement depicting a house in a suburban neighborhood. Sarah is giving him drawing instructions. He's now drawn a sketch of Chuck, Sarah, a dog and a picket fence. Chuck then adds a baby to the arms of the Sarah drawing. Sarah smiles and says "someday." They kiss and Sarah's phone buzzes. It's Casey. He needs a break. Chuck and Sarah enter the train's cargo car and find Quinn's casket empty. They turn around and find Casey in the shadows pointing a gun at them. He tells them, "His men have Alex. I'm sorry. I got no choice."
Speaking in an almost robotic tone, Casey tells Sarah and Chuck to follow him. It turns out Quinn is speaking to Casey via earpiece. Casey is repeating Quinn's orders. He tells Chuck and Sarah to do what he says and nobody gets hurt. Quinn is in the dining car amidst other passengers and watching Casey via a laptop. He orders Casey to go to the control panel and shut down the dining room so he can have some privacy. When they get to a corner out of Quinn's camera view, Casey whispers to Chuck to text Morgan so he can find Alex and get her to safety. At Castle, Morgan is confused by Chuck's text that reads "Alex in danger. Get her to Castle ASAP" because he assumes she never left Castle. Awesome points out she isn't there and went upstairs to the Buy More to get his pizza combos and should have returned by now. Morgan goes to a Castle computer and brings up the Buy More's surveillance footage and watches Alex getting captured by the two "nurses."
Alex is handcuffed in the back of the flu shot bus. Bobbi, the female "nurse" is holding her at gunpoint while Ron, the male "nurse" is having trouble starting the bus. Impatient, Bobbi wonders what's taking so long. Ron doesn't know why the bus won't start. Cut to the open gas tank, covered in sugar granules with a trail on the ground leading to Jeff and Lester hiding behind a car in the parking lot. Jeff wonders what Lester did to the bus. Lester "sugared" their gas tank. The bus is incapacitated, and they now need a plan.
Casey leads Chuck and Sarah down a train hallway towards the dining room car door. They're whispering to each other about how they can handle whatever is behind that door. Chuck tells Sarah how much he really wants the house, the dog and the baby. Sarah wants it too. She tells him, "Let's wrap this up in a bow. Take out Quinn, save Alex." They enter the dining car and find Quinn drinking tea. He gets to the point and tells him he wants the Intersect technology. Sarah tells him if they release Alex, she'll give him the glasses. Just then, Quinn pulls out the glasses from his pocket. Casey fetched them for him, and they're worthless. One of them must have the Intersect.
Sarah points out to Quinn that because one of them has the Intersect, he's now outgunned. And Casey won't shoot them. He tells them if he doesn't call his men on the half hour, Alex will be "sprayed with bullets." Casey reminds Quinn the half hour is coming up. He brought Chuck and Sarah to him, so he should call his men. Quinn brings out a machine gun and tells them that whoever among them has the Intersect is going to help him. They'll retrieve a clean version from a government facility, which would normally be impossible, but there's a chance with the help of the Intersect. During Quinn's speech, Chuck managed to grab a pair of chopsticks from the dining table next to him and tucked them into Sarah's back pocket.
Again Casey urges Quinn to call his men. Quinn finally makes the call and tells Casey that Alex now has another half hour. Casey tells him a half hour is an eternity. He'll think of a way to save her. Quinn, alarmed, raises his gun up to Casey. Sarah flashes and grabs one of the chopsticks in her back pocket and throws it at Quinn who fires erratically through the dining car, blowing out several windows. Sarah flashes again and starts to beat up Quinn. Despite the cries from Chuck and Casey, she doesn't stop and eventually throws Quinn out of a smashed train window. Even after the confrontation however, Sarah continues to flash. She falls to the ground writhing in pain.
Sarah sits with an ice pack on her head while Chuck tries to comfort her. She tells him she tried to stop flashing but couldn't. She's lost control of it. Meanwhile, Casey is on the phone talking to Morgan, trying to formulate a plan. Ellie calls Chuck, who's been working on trying to figure out what happened with Sarah's Intersect. She thinks the amount of flashing she's doing is having an effect on her motor control and causing a migraine. She's also pretty certain that's what caused Morgan's memory loss. Sarah has flashed 40 times in two days, which has probably lead to her loss of control and painful migraine.
Morgan is on the phone with Casey formulating a plan to rescue Alex. He's in the Buy More parking lot with Awesome scoping out the flu bus. Morgan's not sure what to do and wonders why Casey just doesn't call in the CIA. Casey tells him there's no time. He tells Morgan he's going to start a firefight and orders him to go to his Crown Vic and open the trunk. Meanwhile Ellie tells Chuck to put a blindfold on Sarah to prevent flashing because she can't react to what she can't see. She tells him there might be a way for him to build a suppression device. Beckman sent her blueprints, and she begins an upload to Chuck, although he's not sure he can build one. If he was at the Buy More, he could have all the components in seconds. Just then, he realizes he's on a train full of Japanese people. He can steal what he needs from them.
Casey tells Morgan Quinn's men are expecting a call in 19 minutes or they kill Alex. He must save Alex. Morgan promises he will, noting the last words he shared with her won't be a request for pizza combos. Chuck walks through the train and steals the components he needs: a PSP, a laptop and a pair of sunglasses. While returning to the car where Sarah is waiting, he walks over a grate in the floor of the train where we see Quinn holding on for dear life. He didn't fall of the train after all! Back at Casey's Crown Vic, Awesome and Morgan open the trunk to find an arsenal. Casey instructs Morgan to put on one of the earpieces so they can communicate. He tells Morgan to grab a rifle and a knife but to the leave the heavy duty stuff because "you'll only blow yourselves up."
Back on the train, Chuck is trying to engage the hastily built suppression device to help Sarah. Ellie begins the upload of the device plans. During the process, Sarah admits to Chuck and Casey that she doesn't remember anyone named Alex. Chuck is concerned, and to make sure she hasn't forgotten everything, he takes out the sketch he drew earlier and shows it to Sarah. She does remember, saying, "I wouldn't forget that." Chuck assures her everything is going to be fine. Casey gets a call from Morgan telling him they're ready to try to save Alex. Casey tells him to take cover. He tells Morgan to have Awesome call them out of the flu bus while Morgan handles the sniper duties. Just when they're ready to move in, Ron the male nurse puts a gun to Awesome's head. They've been had. Morgan drops his earpiece.
Lester picks up Morgan's earpiece and hears a panicked Casey barking orders to Morgan. A somber Casey tells Chuck that Jeff and Lester are their last hope to save Alex. Chuck tells him that, despite their shortcomings, they're loyal guys. He believes they can save Alex. Having no other option, Casey tells Lester the truth about himself, Chuck and Sarah. They're CIA. After some initial reluctance from Lester, Casey tells him to go to his Crown Vic and grab a couple of pistols but to leave the heavy stuff. Elsewhere on the train, Quinn emerges unscathed from a hatch in one of the passenger cars.
Morgan, Alex and Awesome are tied up in the flu bus. Bobbi and Ron are about to kill all of them because they haven't received a call from Quinn. Just then, a voice booms from the bus' internal public address system telling them to surrender immediately. Ron steps outside to check, and Lester emerges fully loaded with a Gatling gun and assorted heavy artillery whilst chomping on a cigar. At first, Ron refuses to surrender, but when Jeff shows up with a flamethrower declaring, "Behold the flame of destiny," Ron puts his hands up. With Bobbi and Ron captured and tied up, Morgan asks Jeff and Lester how he can ever repay them. Jeff tells him honesty would help. Morgan agrees and takes them to Castle, finally confirming their suspicions.
On the train, the wireless Internet connection stops working just as Ellie's Intersect suppression blueprints upload is nearly complete. Chuck leaves Sarah with Casey to go check out the problem. While checking one of the train's control panels, he discovers it's been tampered with. Quinn sneaks up behind him and wraps a garrote around his neck in a chokehold. Chuck resists, and a battle between Chuck and Quinn ensues. Meanwhile Sarah and Casey are worried that Chuck is taking so long. Sarah tells Casey if he doesn't go check on him, she will. Casey leaves and walks in on the fight between Chuck and Quinn. He points a gun at Quinn and tells him to freeze. Outnumbered, Quinn takes a hostage and points a knife to his neck. Chuck tells him there's nowhere for him to run and to give up; it's over. Quinn responds by saying until the Intersect is his, it's never over. He quickly releases the hostage and gets away. Chuck tells Sarah via earpiece they're looking for Quinn. She gets up and leaves the car.
Quinn makes it to the cargo car. Sarah arrives and tells Quinn, "You won't survive this time." Chuck and Casey arrive but can't get into the car because Quinn has locked it. They both witness Sarah get shot with a dart from Quinn's gun. Incapacitated, Sarah is unable to stop Quinn as he decouples the cargo car from the rest of the train. Chuck and Casey watch helpless as the car fades into the distance. Later, Sarah awakens tied up in an abandoned warehouse. Quinn tells her he's going to remove the corrupt Intersect from her head and have her steal a clean version. She tells him she'll never work for him and secretly activates her tracking device. Quinn reminds her that continuous flashing will give her amnesia, and he's going to induce more flashing with special "flashcards." Quinn starts to show Sarah the cards, and she winces in pain as she begins to repeatedly flash.
At Castle, Chuck is trying to figure out from which facility Quinn plans to steal the Intersect. Casey runs in to tell him Sarah activated her tracking device, and she's nearby. Chuck, Casey and Morgan pinpoint her location and arrive to find that she and Quinn are gone. Chuck finds a note from Quinn that says only "nice try." Chuck is distraught. Sarah wakes up in the hotel room where she used to live five years ago. There's a knock at the door. She grabs her gun and slowly opens the door. It's Quinn with his hands up. Sarah asks who he is and he answers, "Nicholas Quinn? Your handler? We've only been working together five years." He tells her she took a nasty blow to the head and was in the hospital for a week. He tells her orders are in and holds up a photograph of Chuck and asks her if she knows the face. Sarah answers, "Never seen him before." Quinn tells her he's the reason her last mission went south and orders are to kill him. Sarah's now a soldier for Quinn.