Walter White and Jesse Pinkman, barely able to refrain from vomiting, scrub up the hydrofluoric acid-dissolved remains of Emilio Koyama. The grisly scene at Jesse's house takes Walt back to his younger days. In a flashback, he is seen in a laboratory with a female lab partner and they 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's older self flushes another bloody bucketful down the toilet.
At Walt's house, Skyler White and Walter White Jr. are painting a room as Marie looks on. Walt Jr.'s cell phone rings and he departs. Skyler tells her sister that she's writing a story with a stoner character and asks her about marijuana. Marie deduces that Walt Jr. is a pothead. Skyler insists she's only talking about a character, but Marie isn't buying it.
Back at home, Jesse sneaks into the bathroom to smoke meth. Down in the basement, Krazy 8, the cousin of Jesse's former partner Emilio, is shackled to a pipe by a bike lock around his throat. He startles Walt by calling him by name and revealing other details about Walt that Jesse has apparently told him. Walt storms off to find Jesse. High on meth, Jesse refuses to let Walt in the bathroom, so Walt kicks the door down, screaming at Jesse for being a blabbermouth.
The two scuffle over a bag of meth, which Jesse tosses out the window. Walt has a coughing attack while chasing him down the stairs and he barely recovers in time to catch Jesse after he has jumped into his car. Walt says there's more work to do, but Jesse disagrees, "We flipped a coin, you and me! Coin flip is sacred! Your job is waiting for you in the basement."
Elsewhere in the city, Hank Schrader interrupts a drug bust he's conducting to respond to a phone call from Marie Schrader. She tells him Walt Jr. is smoking pot and that Hank needs to scare the kid straight. Although Hank thinks that's Walt's job, he agrees to talk to Walter, Jr.
Hank drives Walt Jr. to "The Crystal Palace," a rundown motel patronized by meth heads and prostitutes. When the boy starts laughing, Hank warns him that pot is a gateway to heavy drugs. He calls over a trampy-looking prostitute, Wendy, to try to prove his point and gets her to show Walt Jr. how meth has corroded her teeth. Disgusted, Hank finally tells her to get lost, adding that if he sees her working there again, he'll bust her. She stumbles off and enters one of the motel rooms 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. The sole entry in the "Kill Him" column: "He'll kill your entire family if you let him go." Walt calls Skyler to explain why he's running late, but she catches him in a lie. She knows he's been fired from the carwash and she tells him to spend the night wherever he is. He makes Krazy-8 a sandwich but collapses on the basement floor while delivering it, shattering the plate.
After regaining consciousness, Walt tells Krazy-8 he has lung cancer, scoops up the plate shards, and leaves to make another sandwich. Upon returning, Walt tries to get to know Krazy-8, who advises Walt that this won't make killing him any easier. Walt acknowledges that he's looking for a reason to spare Krazy-8. "Sell me," he implores.
Krazy-8 tells Walt about college and his musical aspirations. The two make an emotional connection as Krazy-8 reminisces about being the son of a local furniture-store magnate seen on late-night television commercials. Walt recalls buying a crib for Walter Jr. from the same store. When Krazy-8 asks Walt whether he's told his family about the cancer diagnosis and the answer is no, Krazy-8 figures out that Walt is cooking meth so he can leave money for his family. He offers to write Walt a check then suggests Walt isn't cut out for murder. After Walt says he'll get the bike-lock key upstairs, Krazy-8 lets out a sigh.
Upstairs 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 from the plate's remains. 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. As Krazy flails wildly, the improvised knife hits home, stabbing Walt in the leg before Krazy-8 finally expires.
It's a sunny suburban morning when Jesse returns home to find everything perfectly cleaned up. In the basement, he finds the bike lock but no trace of Krazy-8.
Out in the desert, Hank's DEA team has uncovered Walt and Jesse's "cook site." He and his partner, Steven Gomez, quickly put together a theory: a mobile meth lab caught fire, and after putting out the blaze the occupants sped off. But a low-rider car has been left behind, and Hank wonders why until he discovers some meth hidden behind the stereo. Gomez confirms: "Somebody croaked our snitch."
Parked on the shoulder of a freeway overpass, Walt sits in his car and resumes his reverie about human chemistry. Something's missing, his younger self says, about the minute percentage of bodily chemicals he and his classmate can't account for. "What about the soul?" she asks. He chuckles. "There's nothing but chemistry here," he replies, slowly walking up to her and leaning forward, as if to give her a kiss. Back on the overpass, Walt starts his car and drives away.
At his house Walt finds Skyler sobbing in their bedroom, her back to him. "Skyler," he says softly. "There's something I have to tell you."
- 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) "Cat's in the Bag..., 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 remniscient of Vincent and Jules in the film Pulp Fiction.
- The scene between Walt and Gretchen, 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. Hes looking down I-25 from the Bobby Foster Rd Overpass. Billboards and the 2 lanes eastbound and 1 lane westbound helped to locate it.
- "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.
- "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)