In the present, at Gale’s apartment, Jesse shoots Gale and flees. Victor finds a shell-shocked Jesse in the parking lot and returns him to the superlab at gunpoint. Victor admits to Mike that Gale’s neighbors saw him at the scene, but insists it’s not a problem.
Walt and Jesse wait, helplessly, for Gus to arrive. When he does Walt tries to talk his way out of what he’s sure must be a death sentence. Gus seems unmoved… but then slices Victor’s throat with a box cutter, killing him. Then he coldly orders Walt and Jesse back to work.
Later, at Gale’s apartment, police process evidence that includes Gale’s lab notes.
Free, but feeling the looming threat of Gus, Walt purchases a gun for protection. Reeling from Gale’s murder, Jesse throws a raging party to numb himself. Meanwhile, Skyler tries to negotiate the purchase of the car wash Walt once worked at from Bogdan, who refuses because of a grudge against Walt.
Walt urges Mike to help him kill Gus, but Mike lays him out in response: no go. Skyler begs Walt to seek police protection; Walt refuses.
Hank, frustrated by his slow recovery, snipes at Marie, who soothes herself by stealing knickknacks at open houses. After she’s caught, Hank’s detective friend, Tim, resolves the matter. Tim then, based on Hank’s expertise, asks for his help in solving Gale’s murder, leaving him a copy of the lab notes to examine, which eventually he does.
Skyler manipulates Bogdan into selling the car wash, then invents a gambling-addiction story for she and Walt to present to their family in order to explain their ability to purchase it.
Walt discovers that Hank is looking into Gale’s murder, and that he suspects Gale may be Heisenberg. Hank also discloses that Gale’s lab notes contain the blue meth formula, and that fingerprints were found at the murder scene.
Jesse shrugs off Walt’s news about the fingerprints and barely reacts when a partygoer steals his money. His house has become less a party than a crack house; he’s totally numb. Mike reports Jesse’s reckless behavior to Gus and the next day drives Jesse into the desert.
Walt, frantic over Jesse’s disappearance, storms into Los Pollos Hermanos to confront Gus, who’s not there. Mike orders Walt to cook alone.
Jesse complains of boredom as Mike retrieves stashes of cash at various blind drops. He then ends up foiling what looks like an attempted robbery. Jesse is unaware that Gus orchestrated the incident.
Hank withdraws from consulting on Gale’s case citing his feeling of closure. At dinner, Walt, tipsy, can’t stand hearing Hank give Gale all the credit. He speculates that Heisenberg remains at-large, reigniting Hank’s interest.
Cartel gunmen hijack a Los Pollos truck and leave behind a message: “Ready to talk?”
Skyler theorizes that Walt fears for his life and secretly wants to get caught. “I am not in danger,” Walt snarls. “I am the danger.” Scared for her family, she travels out of town to the Four Corners monument to try to decide whether to run or stay; reluctantly she decides to stay in New Mexico.
Walt talks to Saul about his options. Saul tells him if he needs to get out, he knows a guy who can “disappear” him and his family. Walt asks about hiring a hit man to kill Gus, but Saul points out that Jesse already has access. Walt convinces Jesse that Gus must die and prepares ricin to poison him.
Jesse returns to his NA meeting and confesses to killing a “problem dog” — Gale. When the group leader refuses to judge him, he taunts him saying he’d only gone to meetings to sell the members meth.
At the factory farm, Jesse passes up an opportunity to murder Gus. Gus has other problems, facing a cartel representative named Gaff. Gus offers $50 million to cease business relations. Gaff rejects it: “this is not a negotiation,” he says.
Hank presents a startling hypothesis to DEA colleague Gomez and ASAC Merkert: Gus Fring, community leader, is a major meth distributor. They balk at the evidence Hank presents until he drops the bomb: Gus’s fingerprints were found in Gale’s apartment.
Gus deftly handles joint questioning by the Albuquerque police and the DEA about Gale, though Hank unnerves Gus by asking about his Chilean background. The DEA buys Gus’ store and lets him off clean. Hank, however, isn’t satisfied.
Hank asks Walt to drive him to Los Pollos Hermanos and reiterates his theory about Gus before coaxing Walt to plant a GPS on Gus’s car. Walt anxiously admits Hank’s plan to Gus, who seems unfazed and tells him to go through with it.
Gus removes the GPS before visiting Hector “Tio” Salamanca at a nursing home. While there, Gus’s memory drifts back to Mexico in 1989, when Gus and Max, his friend and first business partner in the meth trade, pitched their product at the hacienda of cartel boss Don Eladio. Don Eladio, infuriated by their presumption, has Tio kill Max and forces Gus to watch.
Walt warns Mike that Hank has discovered the factory farm and plans to stake it out. Jesse and some of Mike’s henchmen remove evidence of meth distribution from the location before Hank can get there, but afterward a cartel sniper (Gaff) opens fire on them and shoots one of Mike’s men. Gus strides out into the sniper fire, defiant, but that night, calls the cartel: he’ll give them what they want.
The IRS audits Beneke Fabricators. As Ted‘s former bookkeeper, Skyler fears that her finances could come under scrutiny, so she plays dumb and convinces the agent that Ted’s mistakes are all innocent. All Ted needs to do is pay back taxes and penalties; unfortunately, he’s broke. Out of the frying pan…
Gus asks Jesse if he can cook Walt’s formula. Jesse accuses Gus of planning to murder Walt. Gus replies that he needs Jesse’s help to prevent war with the cartel.
Jesse begs Walt to coach him on using his meth formula for the cartel chemists. Walt accuses Jesse of switching his allegiance and never intending to kill Gus. Walt then reveals that he’s been keeping tabs on Jesse, and tells him he hopes Jesse ends up dead in the Mexican desert. Jesse explodes and they have a knock-down drag-out fight. In the end, Jesse kicks Walt out and tells him never to come back.
In Mexico, Jesse faces down the cartel’s lead chemist and cooks a high-quality batch. Back in Albuquerque, Skyler — through Saul — provides Ted money to cover his IRS debt, but Ted still refuses to settle his debt.
Back at Don Eladio’s, Gus offers a gift of tequila laced with poison. Don Eladio and his entourage drink it and collapse. Jesse helps Mike evacuate Gus, who drank the tequila to fool Don Eladio and, despite inducing vomiting, is feeling the effects of the poison. In the escape, Mike is shot and Jesse kills the shooter.
Gus recovers at a state-of-the-art, though makeshift, medical facility that he set up in advance of their trip. Back in Albuquerque, Gus gloats to Tio that the cartel is destroyed and that Jesse shot Tio’s grandson, thus ending the Salamanca line. He finally has his vengeance for Max’s death.
Hank asks Walt to drive him to the industrial laundry. Fearing exposure, Walt deliberately causes an accident, laying Hank up for awhile. He’s bought some time, but Hank’s not deterred.
Saul’s men force Ted to pay his IRS tab. Trying to escape, Ted cracks his head on a kitchen counter, badly injuring him.
Jesse’s ex-girlfriend Andrea and her son Brock are at Jesse’s house when Walt comes to beg for help. Jesse rejects him. Gus’s operative Tyrus tasers Walt and transports him to the desert, where Gus fires him. After Walt mocks Gus’s failed attempts to turn Jesse against him, Gus threatens Walt’s family: he’s going to kill Hank, and if Walt interferes, he and his entire family will die. With no value left to Gus, Walt thinks he’s a dead man.
Walt rushes to Saul’s to get in touch with the “disappearer.” Saul agrees to warn the DEA about the danger to Hank. Walt then learns that Skyler gave Ted most of their money to pay his taxes, leaving them without enough to pay the “disappearer.” With Hank alerted, Gus will now know Walt talked, and set his sights on killing Walt and his family.
The DEA provides protection for Hank, Marie, and Walt’s family at the Schrader home though Walt refuses to stay there himself. Walt heads off to figure out what to do. He spins a gun in his back yard, possibly thinking of killing himself. In the end, he gets an idea and heads out.
Brock is hospitalized for a flulike ailment. After discovering his ricin is missing, Jesse tells Andrea to alert the doctors about a possible poisoning, and goes to confront Walt.
Jesse accuses Walt at gunpoint of poisoning Brock, but Walt convinces Jesse that Gus framed him: he claims Gus is using Jesse as the perfect assassin to kill Walt. Walt and Jesse conspire to eliminate Gus by luring him out into the open, but Walt’s car bomb fails when Gus senses something amiss and abandons his car at the hospital parking structure.
Suspicious about Jesse’s ricin theory, two detectives question him. Saul visits Jesse at the station and passes Walt a message from Jesse about Gus’s visits to Tio. Walt deduces that the men are enemies and persuades Tio to entrap Gus. Tio goes to the DEA with the ruse of being an informant — in actuality, Tio merely insults and taunts the agents.
The police release Jesse after Brock tests negative for ricin. Outside the station, two men kidnap Jesse and force him to cook at the super-lab again, handcuffed and with a gun virtually to his head.
Gus visits Tio and calls him a “crippled rata” for talking to the DEA. As Gus prepares to administer a fatal injection, Tio detonates a bomb Walt installed under his wheelchair. Gus, Tio, and Tyrus are blown to pieces.
At the superlab, Walt kills Jesse’s captors, and he and Jesse torch the lab.
Later, Jesse tells Walt that the common plant Lily of the Valley poisoned Brock, not ricin. “But still, he had to go, right?” asks Jesse of Gus.
“You’re damn right,” Walt replies. They shake hands, and Jesse returns to the hospital to be with Brock and Andrea.
Walt calls Skyler; she’s seen the news about the explosion and wants to know what happened. “I won,” he says, simply.
Walt drives out of the parking structure past Gus’ deserted car.
A flowering plant sits poolside at Walt’s house. The tag reveals its name: Lily of the Valley.