Walter White races through busy Albuquerque streets, dodging traffic while shouting instructions to Saul Goodman on his cell phone. If Walt doesn't return within 24 hours, Saul is to deliver all of Walt's money to Skyler White. Walt then calls Skyler and leaves a hurried message but trying not to sound desperate, telling her he loves her: evidently, Walt is heading into some kind of showdown and is aware he might not come out of it alive. He places his gun on the front passenger seat next to him in anticipation...
Armed with his .38, Walt storms into Los Pollos Hermanos and demands to speak with Gustavo Fring. The manager says that Gus isn't there, but Walt doesn't believe her. He states that he's seen Gus's car parked outside so he'll wait until Gus is called out.
While he waits, Mike Ehrmantraut calls him to ask what he's doing, then tells him that Jesse Pinkman will be with him for the day, and puts a blase Jesse on the phone when Walt insists on speaking to him. Jesse confirms he's ok, does not have a gun pointed at him, but doesn't know where they're going. Mike then tells Walt that today he'll just have to handle the cook alone. Walt pushes his way into Gus' office only to be surprised that it's empty.
Out in the desert, Mike drives up a long dirt road. Despite seeming not to care whether he lives or dies, Walt's worry has set Jesse on edge so he positions his keys between his fingers to use as a probable weapon. He watches nervously as Mike exits the car and grabs a shovel from the trunk. Is this it? But Mike passes Jesse by and starts digging. After a few moments, Mike pulls a bag of money out of the ground and tosses it in the trunk. Mike tells Jesse that they have six more collections to make today and he wants to have it done before dark.
At home, Hank Schrader jokes with Tim about the oddball personality that Gale's notebook evokes: "it's like Scarface had sex with Mr. Rogers." He then identifies Badger and Jesse as the only people directly tied to the blue meth that he knows of. Hank admits to having "a history" with Jesse (referring to the savage beat-down he delivered last season) but doubts that Jesse murdered Gale.
Mike makes his next pickup at an abandoned warehouse and finds Jesse standing guard when he returns to the car. As the pickups—shown in a sped-up montage set to humorous music—continue, Jesse becomes increasingly bored and frustrated. If he's riding shotgun as "the guy" on this assignment, then Mike should tell him what they're doing and why, or at very least get a little conversation going to help relieve his boredom. Mike abruptly pulls the car over and barks that in no way is Jesse "the guy" (implying that Victor, whom Gus killed, had been his guy). There may be some reason Gus has for sending Jesse on this mission, but Mike does not know it.
In the lab, Walt has difficulty managing both his and Jesse's portions of the prep work. After starting the cook Walt returns home to sign papers finalizing the loan to buy the car wash. For them to succeed going forward, Skyler tells Walt, they have to be completely honest with each other. Skyler then plays her phone messages and hears Walt say that he loves her. The two stare at each other meaningfully for a moment, then rush into the bedroom in the heat of passion.
Later, Walter Jr. arrives home and realizes that his parents are having (or just had) sex. Skyler frets over Walter Jr.'s reaction and suggests that Walt move back home so it's easier to explain to everyone. Walt kisses Skyler in reply.
Later, back at the lab, Walt drops a barrel of methylamine while struggling with the forklift. Fed up, he screams at the security camera that the cook is a two-man job. He's not cooking anything until Jesse returns. A while later Tyrus Kitt arrives at the lab and operates the forklift for Walt. Jesse's not coming just because Walt asks for him.
Mike makes the final pickup of the evening at another abandoned warehouse. While he's inside, a second vehicle arrives, and Jesse notices one of its occupants approaching Mike's car with a shotgun. Jesse, convinced Mike is about to be robbed (or finally be "offed"), shifts into reverse, floors it, knocks the gunman to the ground, and slams into the other car. Then he peels out in an attempt to lose the gunman and his cohort. A bit later, Jesse catches up with Mike elsewhere walking in town, picks him up, and explains what went down outside the warehouse.
Later at the lab, Jesse tells Walt that he spent the previous day guarding Mike and bristles when Walt makes light of the notion. Mike and Gus rendezvous outside Los Pollos Hermanos. Everything with Jesse went the way Gus planned, Mike reports. The gunman clearly was a plant, and Gus set it all up for Jesse's benefit.
At Hank and Marie's house for dinner, Walt anxiously swills wine in the kitchen as Skyler discusses the car wash. When Hank jokingly refers to Walt as famous card shark "Nick the Greek," Marie criticizes him for enabling Walt's gambling addiction. Walter Jr. changes the subject to the Boetticher case. Hank says that he's stopped working on it, but praises Gale as not merely a cook, a bona fide genius: That if he had set his mind to something good, who knows what he'd be able to achieve to help people. Walt, increasingly irate from Hank's assertions and by now a little tipsy, can't let someone else take credit for his work. He dismisses the "Lab Notes" journal as "simple rote copying, probably of someone else's work." Skyler looks on disbelievingly as Walt muses that "this genius" of Hank's might still be at large.
The next morning, Hank tells Marie—in a more polite tone than he's used with her in quite some time, even apologizing for making a small mess on the kitchen table—that he's resumed looking into the Boetticher case. Looking through police photographs taken in Gale's apartment, Hank notices a napkin from Los Pollos Hermanos, with some letters and numbers — perhaps a serial or model number for some product — inked at the bottom.
- The episode title, "Shotgun" is a reference to both Jesse riding shotgun with Mike and to the shotgun the attacker is holding when approaching Jesse.
- There's a slight reference to the pilot episode of the show in this episode. At the table, Hank says "I've got your wipe-down right here" and grabs his crotch; this is very similar to what Walter said and did to Bogdan as he was leaving the job.
- During the musical cue ("1977" by Ana Tijoux) Jesse, while bored, mindlessly taps Mike's dashboard and sings: "Fallacies, fallacies, one for you, and two for me" a line from Fallacies by TwaüghtHammër. He previously sang this exact same line in the superlab ("") while mindlessly zipping the zipper of his protective suit up and down, also while bored, also during a musical cue ("Shimmy Shimmy Ya" by Prince Fatty feat. Horseman).
- Production error: when Mike and Jesse drive to the desert at the beginning of the episode on a dirt road you can see a camera and a guy behind it shooting the scene. (minute 8:57)
- Mike and Jesse visit several drop sites, including: a deserted windmill, an abandoned warehouse, and a burned down building.
- Walt's ineptitude in using the forklift, dropping the chemical barrel and letting it roll, is the mirror of his and Jesse's inability to handle their first drum, which they carried instead of rolling.
- Saul doesn't physically appear in this episode, although Walt speaks to him on the phone.
- Continuity error: When Walt walks into Los Pollos Hermanos, a poster can be seen on the wall near the door showing an award the restaurant received for “Best Burrito 2010”. However, this episode is estimated to have taken place in 2009.
- "Aztek" by Dave Porter (as Walt drives from the superlab to Pollos Hermanos)
- "1977" by Ana Tijoux (during the montage of the pickups and that of Walt cooking alone)
- "The 808 Track" by Bassnectar (when Jesse turns on the radio during the pickups montage)
- "Fallacies" by TwaüghtHammër, performed by Aaron Paul as Jesse (while he waits in the car during the final pickup)
- "Corrido de Tiburcio Calderon" by Arturo Salas (playing from Garcia's diner as Mike meets up with Jesse after the attack)
- "Unknown Track #4" by Unknown Artist (playing in Jesse's earphones as Walt arrives at the lab)
- Mike: "You are not the guy. You're not capable of being the guy. I had a guy, but now I don't. You are not the guy."
- Jesse: "Then what the hell am I doing here?"
- Mike: "I don't know."
- ―Mike and Jesse. Mike line is notably also used in the Breaking Bad remix