As Walt and Jesse are scrubbing up the dissolved remains of Emilio, the grisly scene takes Walt back to his days as a graduate student. In a flashback, Walt and a female lab partner are analyzing the human body's chemical composition. After discovering that only 99 percent of the body's makeup is accounted for chemically, Walt muses that there has to be more to a human being than that. Back in the present, Walt flushes a bloody bucketful down the toilet.
At the White residence, Skyler and Junior are painting the new baby's room as Marie looks on. Junior's cell phone rings and he departs. Having been told by Walt that he has been smoking marijuana, Skyler tells her sister that she's writing a story with a stoner character and asks her about pot. Marie assumes the question that Junior is a pothead. Skyler insists she's only talking about a fictional character, but Marie isn't buying it.
At Jesse's house, Jesse sneaks into the bathroom to smoke meth. In the basement, Krazy-8, who remains shackled to the pipe, startles Walt by addressing him by name and revealing personal details that Jesse has apparently told him. Walt angrily goes up to the upstairs bathroom to confront Jesse, who is high and refuses to let him enter. Walt kicks the door down. A scuffle ensues over Jesse's bag of meth, which he tosses out the window. Walt has a coughing attack while chasing Jesse downstairs and barely recovers in time to catch him before he drives off in his car. Walt says there's more work to do, but Jesse leaves.
Marie phones Hank in the middle of a drug bust, convinced that Junior is smoking pot and that Hank needs to scare him straight. While initially reluctant, Hank drives Junior to "The Crystal Palace," a local roach motel patronized by meth heads and prostitutes. Hank warns Junior that pot is a gateway to heavy drugs. He tries to prove his point by calling over a disheveled prostitute, Wendy, and showing Junior how meth has corroded her teeth. Disgusted, Hank threatens to bust Wendy if he sees her working there again. Wendy stumbles off and enters a motel room, where she meets Jesse and they have sex.
Walt sits on the toilet in Jesse's bathroom, jotting down the pros and cons of killing Krazy-8. He comes up with several arguments in support of clemency, while the sole entry in the "Kill Him" column is, "He'll kill your entire family if you let him go." Walt calls Skyler to claim he is running late at the car wash, but learns that she already knows he's been fired from that job. An angered Skyler tells Walt to spend the night wherever he is. Walt makes a sandwich for Krazy-8 but collapses on the basement floor while delivering it, shattering the plate.
After regaining consciousness, Walt tells Krazy-8 that he has lung cancer, scoops up the plate shards, and leaves to make another sandwich. Upon returning, he tries to get to know Krazy-8, who tells Walt that doing so won't make killing him any easier. Walt admits that he is looking for a reason to spare Krazy-8. The two seem to bond as Krazy-8 reminisces about being the son of a local furniture-store owner whose commercials air on late-night television. Walt recalls buying a crib for Junior from the same store. When Walt admits to Krazy-8 that he hasn't told his family about the cancer diagnosis, Krazy-8 deduces that Walt is cooking meth so he can leave money for his family. Krazy-8 offers to write Walt a check, then suggests he isn't cut out for murder. When Walt leaves to retrieve the key to the bike lock, Krazy-8 seems relieved.
Walt gets the key, but a sudden inspiration prompts him to piece the broken plate back together; he realizes a large knife-shaped shard is missing. Back downstairs, Krazy-8 stands quietly as Walt approaches and motions his hostage to turn around so he can slip the key into the lock. When Walt hesitates, Krazy-8 gently commands him to unlock it. As Walt grasps the lock, he asks Krazy-8 if he's going stab him with the shard once set free. Krazy-8 stabs backward wildly and Walt pulls back hard on the lock, strangling him. As Krazy-8 flails wildly, he manages to stab Walt in the leg before finally expiring. Walt tearfully apologizes to Krazy-8 as he dies.
The following morning, Jesse returns home to find Krazy-8 missing from the basement and the bike lock left behind. Meanwhile, the DEA discover Walt and Jesse's cook site in the desert. Hank and Gomez quickly put together a theory that a mobile meth lab caught fire and that the occupants sped off after putting out the fire. However, Krazy-8's low-rider car has been left behind. Hank wonders why until he discovers meth hidden behind the stereo.
Parking his Aztek on the shoulder of a freeway overpass, Walt sits and resumes his flashback to discussing human chemistry with his lab partner. Returning home, Walt finds Skyler sobbing in their bedroom. He then informs here that there is something he has to tell her, alluding to his lung cancer diagnosis.
- Uncensored on home video. Jesse says, "Fucking do it already." Krazy-8 tells Walt, "Up until the day I said, 'Fuck you,' and quit."
- The title (completed from Episode 2) """, and the bag's in the river" is a quote from the film Sweet Smell of Success (1957), spoken in reassurance that a situation is being handled. The toilet that Walt flushes the blood bucket contents down can be thought of as a metaphorical river.
- Walt is using baking soda to clean up Emilio's body, since baking soda is an alkaline and can neutralize the acid.
- In the next episode, it is revealed that Walt's crib is indeed from Tampico Furniture.
- According to Walt, the human body broken down by chemical element:
- Hydrogen: 63%
- Oxygen: 26%
- Carbon: 9%
- Nitrogen: 1.25%
- Calcium: 0.25%
- Chlorine 0.2%
- Phosphorous 0.19%
- Sodium 0.04%
- Sulfur 0.050002%
- Iron: .00004%
- The scene of Walt washing Emilio's remains off of Jesse's body is reminiscent of Vincent and Jules in the film Pulp Fiction.
- The scene between Walt and Gretchen, at the time his lab assistant, in the teaser is chronologically the first scene of the series, taking place somewhere between 1985 and 1989.
- The Crossroads hotel Hank takes Walt Jr to and where Wendy makes her first appearance is located at 1001 Central Ave NE, Albuquerque in real life. As of 2016 the soda machine at the lobby door no longer there.
- The next to last scene has Walter sitting in his car on an overpass, thinking about the chemical makeup of a body. He's looking down I-25 from the Bobby Foster Rd Overpass. Billboards and the 2 lanes eastbound and 1 lane westbound helped to locate it.
- "Gray Matter" by Dave Porter (playing during the episode teaser and while Walt sits in his car on the highway bridge)
- "Without You" by Sasha Dobson (playing in the store where Marie steals a pair of shoes)
- "The Missing Piece" by Dave Porter (as Walt retrieves the pieces of broken plate from the trash)
- "The Morning After" by Dave Porter (as Jesse returns to his house the morning after Walt has killed Krazy-8)
- "Oh well, heil Hitler, bitch! And let me tell you something else. We flipped a coin, okay? You and me. You and me! Coin flip is sacred! Your job is waiting for you in that basement, as per the coin!"
- ―Jesse Pinkman to Walter White.
- Krazy-8: "Unlock me, Walter."
- Walter: "The moment I do, are you gonna stick me with that broken piece of plate?"
- ―Just before Walt kills Krazy-8 by choking him with the bike lock
- Walter: "I don't know. Just...doesn't it seem like...something's missing?"
- Gretchen: "What about the soul?"
- Walter: "The soul? There's nothing but chemistry here."
- ―Walter and Gretchen discussing about human body composition.