A young boy, Drew Sharp, rides through the desert on a dirtbike. He stops to play with a tarantula, which he then enthusiastically places into a jar. When he gets back on his bike, he hears a freight train in the distance and drives off to follow it.
Walter White visits Hank Schrader in his new ASAC office where Hank remarks on Walt's expensive new watch. Walt lies and tells Hank it's a birthday present he bought for himself. During their brief conversation, Walt breaks down in crocodile tears, telling his brother-in-law that Skyler White no longer loves him and thinks he is a bad father. Uncomfortable with displays of emotion, Hank quickly excuses himself to get them a cup of coffee and to give Walt some space (as Walt, master-manipulator, anticipated Hank would react). Walt seizes the opportunity to plant a transmitter in Hank's computer and a receiver within a family picture frame on his desk.
In the basement of an abandoned building in Houston, Walt and Jesse Pinkman stand by as Mike Ehrmantraut threatens Lydia Rodarte-Quayle. He forces her to call the DEA to sort out the GPS's origins, supplying her with a prepared script, threatening her life if she cries or arouses Hank's suspicions in any way. Listening into Hank's phone communications, the GPS trackers were revealed not to be the work of the Albuquerque DEA Field Office. Discussion among Mike, Walt, and Jesse leads to Jesse dissenting but Walt agreeing with Mike that Lydia be killed, with Lydia insisting that it wasn't her doing and begging for her life to be spared. Just as Mike approaches her, the bug picks up a call from the Houston field office confirming to Hank that they placed GPS tracking devices on the outside of all the methylamine barrels. Mike still wants to kill Lydia, but she saves her life by informing the men of an "ocean" of methylamine in a freight train tanker car that passes through New Mexico each Wednesday. Lydia demands a percentage after providing key transport details to boost the methylamine, including the exact position of that tanker car in the freight's lineup, but Mike is skeptical of their ability to complete the heist without killing the engineer and conductor, which he thinks is the only viable way to get away 'clean'.
At the Schrader house, Hank plays with Holly White as Marie looks on. Hank lovingly tells Holly he's "not going to give her back," and Hank asks Marie how "Emo McGee" is doing. Just as Marie remarks that Walt Jr. is being reclusive and unsocial and Hank replies that his parents treat him like a baby, Walter White Jr., steps out of his temporary bedroom to walk into the kitchen. Marie calls out to him using his current preferred name "Flynn," indicating his defiance once more, again over the temporary relocation and stonewalling by his parents. Hank asks him if he wants to watch the Blu-ray of Heat with him later, and Flynn declines. Marie asks Flynn if he wants some lasagna, and he declines that offer too, angrily telling them he's going back into his room so they can "keep talking about him." Walt, Jr. defiantly returns home sometime later that day. Back at the Whites' house, Skyler stands outside his bedroom door as he refuses to come out. Walt, however, wanting to win Skyler over, uses his parental trump card to order him back to the Schrader house, however Skyler shows absolutely no gratitude towards Walt for doing so. Skyler then expresses her fear of Walt and his profession, tells him she will never change her mind about him, and negotiates a deal with him: if Walt agrees to keep the children away from the house while he's engaging in the drug business, she'll launder the proceeds and do as he pleases. She then refers to herself as Walt's "hostage."
Back at Jesse's House, Mike and Walt argue about how to proceed with production. Jesse once again hangs back on the living room couch, away from the other two as they engage in yet another tense standoff. Mike proposes using pseudoephedrine for the time being, but Walt dissents, suggesting they halt production until they acquire methylamine. The discussion then becomes heated, with Walt accusing Mike of being content to merely scrape together the hazard pay for his and Gus's former associates, and Mike in turn suggesting that Walt actually is willing to go through with the heist, but is waffling about it due to the necessity of killing the two engineers. Jesse, playing with a glass of drink and a straw as the others argue is suddenly inspired and interjects with an idea: what if they can steal it without getting caught? They can plan to stop the train and siphon off a large amount of methylamine and avoid killing the engineers.
At some train tracks in the middle of the desert, Mike, Jesse, and Walt measure off 800 feet, the length to reach the methylamine tanker car in the freight train lineup finding that the length aligns perfectly with a small bridge in the tracks. The operation can be completed and be well-hidden from the train's crew. Fernando & Sandor, trusted crew members from Vamonos Pest, help dig a hole and bury two giant plastic tanks near the tracks. Todd Alquist, another Vamonos crew member fills one with water, its weight approximately 9/10ths of the weight of the methylamine they intend to heist, and the other remains empty. They plan to replace the methylamine with water as the tanker drains, giving the appearance that the Chinese supplier watered down the product, and deterring any indications of theft. Later, Patrick Kuby blocks the train tracks with a dump truck filled with the dirt from the pit they dug for the tanks, and the train screeches to a halt. Mike signals to Walt when the conductor and engineer get out to help Kuby with the truck. Jesse scrambles under the train and begins siphoning methylamine into the empty underground plastic tank. At the same time, Todd climbs atop the train, opening the upper lid with a cordless impact wrench and inserting his line of firehose for the replacement fluid. When the meter by Walt displays over 300 gallons of methylamine has been siphoned off into the first underground tank, Walt turns on the compressor to evacuate the water from the second underground tank, signaling to Todd that the replacement water is coming.
The plan appears to be working, with Mike close by Kuby's truck and with Kuby stalling the engineers, until a Good Samaritan drives up, stops and offers to push Kuby's truck off the tracks. Mike warns Walt to wrap things up, but he waits until the last moment possible to finish the operation, forcing Todd to jump off the moving train and Jesse to lay down flat on the tracks, beneath the train. Walt, Jesse, and Todd celebrate their flawless heist, until they see Drew Sharp, who has just caught his tarantula and driven over to the train and witnessed their brief celebration. The kid nervously waves at the three, who stand in stunned silence staring back. Todd hesitantly returns the wave, then slowly reaches behind his back, pulls a gun he had concealed in his waistband and shoots the boy dead as Jesse yells in protest.
- At the start of the episode, you see the back of Drew Sharp's bike helmet is red with two yellow stripes. Yet when we see the whole body of the boy his helmet is blue with two yellow stripes. The yellow stripes also appear on the back of his helmet too.
- A scene of Walter calculating the gain from the heist (nearly 300 million USD), compared to all historical train robberies is deleted but released on Blu-ray and the Italian version.
- Bob Odenkirk, as Saul Goodman, does not appear in this episode.
- Jesse James is once again mentioned in this episode, this time by Jesse Pinkman when he says that boosting the methylamine from a train is just like "Jesse James." Jesse James was previously brought up when Mike Ehrmantraut compared Walter White's murder of Gustavo Fring to Robert Ford, Jesse James' assassin, saying "Just because you shot Jesse James, don't make you Jesse James." ("")
- The movie Hank says he has on blu ray, Michael Mann's Heat (1995) is a heist film. During the opening heist in which Neil McCauley's crew stages an armored car robbery, one of the thieves, Waingro, executes a guard unnecessarily, and is subsequently dumped by the gang. This parallels the ending of this episode when after the train heist, Todd Alquist shoots the boy, much to the dismay of Mike and Jesse.
- The location for the filming of the train heist outside Santa Fe, New Mexico, is the same location for the filming in 1969 of Butch Cassidy and the Sundance Kid, in which Butch Cassidy and the Sundance Kid jumped out of a passenger train.
- The scene where Mike, Jesse, and Walt are interrogating Lydia is very similiar to the scene in the Season 3 episode, Half Measures when Gus has the meeting with Jesse and the two drug dealers that Walt ends up running over. In that scene, Gus tells Jesse that Walt is his only friend in the room, and when Jesse turns to look at Walt Gus tells him: "Look at me, not him." In the scene with Lydia, Mike tells her that Jesse and Walt are being kind to spare her, and when she turns to look at them Mike tells her: "Look at me, not them."
- The shot of Jesse underneath the train was achieved by visual effects, with two separate shots combined: the train moving and revealing the tracks, and Jesse on the tracks.
- Many crew members working on the episode have said it was very tough to film.
- The episode was originally to be called "Dark Territory", but the name was taken from a movie called Under Siege 2: Dark Territory, which also starred Jonathan Banks in pretty much the same exact role he had in this episode.
- During the scene where Walt bugs Hank's office, on Hank's desk sits a black "Function First Collection" gooseneck table lamp. This may be a subtle reference to The Sopranos, in the episode "Mr. Ruggerio's Neighborhood", where the F.B.I. plants a bug in the exact same type of lamp owned by Tony Soprano.
- The truck used to haul the empty tanks, the dirt, Drew Sharp and his motorbike and block the tracks is an International 9000-Series.
- The earth-mover used to dig the hole for the tanks is a John Deere 310 G.
- In the previous episode "Fifty-One", Walter said: "The methylamine keeps flowing, no matter what. We are not ramping down. We're just getting started. Nothing stops this train." This could be a reference to their train robbery in this episode.
- The train heist was filmed at a location just off US-285 & Spur Ranch Rd. This location is probably one of the furthest from Albuquerque other than the 4 Corners scene. The train bridge is located at 35.498818, -105.916618 and the train crossing where they stall the truck is a few hundred feet away.
- "Dead Freight" by Dave Porter (as the gang rob the train)
- Jesse: "I hate to say it, but she's right, Mike. She saved our asses by finding that thing."
- Mike: "She's saving herself. She's a loose cannon. I am telling you, she will turn a gun or a badge on us the first chance she gets. The woman put a hit out on me."
- Walter: "Seriously?"
- ―Jesse, Walter and Mike discussing the captured Lydia.
- Lydia: "Hey! You still need methylamine, don't you? Right? You wanna talk methylamine? Then tell your partner to stop threatening me, and let's talk."
- Walter: "Talk about what? You heard. You can't even get us a single barrel."
- Lydia: "Who said anything about barrels? I'm talking about an ocean of the stuff."
- ―Lydia bartering with methylamine for her life.