Walt and Jesse continue their work at Gus's superlab. Walt's calculations on their meth yields seem to be off, though: they're coming up consistently short. Jesse suggests spillage, evaporation, and other causes for their product's yield being low, but none of them make sense.
After Jesse punches out for the day, Walt notices a fly in the superlab. Concerned for contamination, Walt tries to kill the fly, but his every attempt fails, with one attempt causing him to fall flat on his ass and get winded and the fly landing on one of the lenses of his glasses, almost as if taunting him...
When Jesse returns to work the next day, he notices Walt's car still parked outside the laundromat. When he enters the lab, his ears pop as a result of increased air pressure that Walt subjected the lab to in order to contain the "contamination". When Walt finally states that the contamination is a simple house fly, Jesse is left gobsmacked: Mr. White is getting this worked up over a fly?! When Jesse tries to cook, Walt commands him to stop, and hits him with his homemade fly swatter. After Jesse whacks Walt in the head with the fly swatter when the fly lands on Walt's head, Walt explains that there is no room for error when dealing with Gus: if they cannot clear out the contamination, they're as good as dead.
Jesse tries to tell Walt that they should step out for air and clear their heads, Walt takes Jesse's lab keys and banishes him from the lab: "If you're not gonna help me, stay out of my way!" he barks. Jesse counters by shutting off the laundromat's main breaker to regain entrance.
When Jesse returns to the lab, he brings fly paper to try and catch the fly. He also brings some sleeping pills to slip into Walt's coffee, so Walt can get some sleep.
While waiting for the fly to get caught by one of the traps, Jesse tells Walt about "Scrabble", a possum that had been found under his aunt's house that used to cause a ruckus. Even after the possum was removed, his aunt was still convinced that "Scrabble" was still under the house making noise. It was a sign that her cancer had metastasized and spread to her brain.
Walt reminds Jesse that he is in remission and, as the sleeping pills begin to take effect, confides in Jesse his desire to die. He was wracked with guilt and sorrow over the lies he had to tell, and the fact that he cannot seem to make Skyler understand that he is cooking meth for the sake of his family. Furthermore, he had met Jane's father on the night that she died: the universe may be random, but how could it be random that he wound up in the exact same bar as Donald Margolis on the very night that Jane overdosed? As he becomes drowsy, he recalls hearing his wife singing a lullaby to their daughter and thought that, at the time, he had made all of the money he had aimed to make and leave for his family; if he had just passed away at that moment, it would've been perfect...
As Jesse spots the fly and prepares to swat it, Walt, half-sleeping, begs Jesse to come down from the ladder and apologizes for Jane. Jesse, not realizing Walt was confessing to letting Jane die, tells him it's not his fault: no one could've stopped Jane from overdosing.
Conceding that their entire cook was contaminated, Walt finally falls asleep. Jesse sees the fly once more, and this time, manages to swat it, killing the pest once and for all.
The two return home the following morning. In the parking lot, Walt pulls Jesse aside and talks to him: he suspects Jesse may be taking some of their product, but didn't want to say anything in the lab in case it was rigged with microphones. While he never outright states that Jesse is stealing their meth for himself, he warns him that if he is and Gus finds out, he wouldn't be able to protect him.
Jesse feigns ignorance before he leaves. Later that night, Walt lies in bed, seemingly unable to sleep, when all of a sudden, a familiar irritating buzzing reaches his ears...
This episode provides examples of:
- Absentee Actor: The entire cast save for Walt and Jesse.
- Bottle Episode: With the exception of the opening and closing scenes, the entire episode takes place inside the lab. Only Walt and Jesse appear in it, although we also hear Skyler's voice through the baby monitor. And even then, it's reused audio from "Phoenix".
- Closed Circle: Jesse and Walt are trapped in an airtight lab trying to kill a fly to prevent contamination; since they can't cook meth with the contaminant, and they can't leave until they've cooked, they spend the episode trapped.
- Death Glare: As seen in the page image, Walt gives the fly in the lab a really mean look when it lands on his glasses.
- Despair Event Horizon: Walt lampshades this while talking to Jesse about finding out about his cancer being in remission. He would've much preferred if he succumbed to the cancer after his daughter's birth. It's implied that this ideal death would enable Walt to avoid any heavy consequences with his drug manufacturing, but with the remission, Walt will probably be alive a little longer than he assumed.
- Does This Remind You of Anything?: Walt is hunting a fly that he views as a filthy contaminant. During the hunt, Jesse dons his safety gear and tries to keep cooking. His facemask is propped in such a way as to put two large, red bulbs on top of his head — just like the fly's eyes. Walt even smacks him with his improvised flyswatter.
- Epic Fail: Walt discovers a housefly in the meth lab. He begins trying to swat the fly, but it's just too fast for him. Growing increasingly frustrated, he spots the fly on the ceiling and throws his shoe at it — and ends up breaking an overhead light, raining glass down on himself and getting his shoe stuck in the light fixture. Then, he goes up on the catwalk and over the railing to dislodge his stuck shoe, spots the fly on the railing he's hanging from and attempts to have a swing at it... and falls off the catwalk, slamming into a vat and landing painfully on the floor. Just to make things worse, the fly then lands on his glasses. That's right: Breaking Bad did slapstick comedy.
- Even Evil Has Standards: Arguably taken too far with Walt, who refuses to cook a batch of methamphetamine — one of the most harmful and addictive drugs that there is — because a fly may contaminate it. Jesse lampshades the absurdity of this:"We're making poison for people who don't care. We probably have the most un-picky customers in the world."
- For Want of a Nail: During the Motive Decay moment listed below, Walt says that he should never have left home and went to Jesse's apartment. He then quietly states that things could've been different if that were the case.
- Here We Go Again!: The episode ends with Walt finding a new fly on his smoke detector.
- In Vino Veritas: When Walt is drowsy thanks to his sleeping pills, he opens up about how he should be dead by now and would have preferred to succumb to his cancer. He also almost tells Jesse his role in Jane's death, but it's subverted when Jessie misunderstands what he was saying.
- The Last of These Is Not Like the Others: In "Fly," Walt tellingly adds the birth of his daughter as an after-thought, seeming to place more importance on the first million he made as a reason to have not dropped dead.
- Locked in a Freezer: Walt and Jesse are trapped in the lab, unable to cook until they manage to decontaminate the lab (i.e., kill one of the most daring flies on television). They're stuck there until they can kill the fly and cook the batch.
- Motive Decay: Pointed out by Walt himself; he only needed enough money to leave behind once he died. Once he went into remission and started working for Gus, it started to not make sense.
- Specifically, Walt states that had he died listening to Skyler singing to Holly over the baby monitor (back in "Phoenix"), then it would've been the "perfect moment" for him to stop.
- Neat Freak: Walt panics over a fly in the lab.
- One Degree of Separation: Walt muses on how unlikely a coincidence it was that he would meet Don Margolis at the bar, even more so given that the very same night, Walt would go on to watch Jane Margolis asphyxiate on her own vomit.
- Obfuscating Insanity: It seemed that Walt was faking his obsession over the fly to draw attention away from him confronting Jesse over some stolen meth. Though in the end when he sees a fly on his smoke detector, he might have not been all the way faking it.
- Serious Business: You can't have a fly in your meth lab; it taints the product.