With a murder investigation on their hands, the police search Gale Boetticher’s (David Costabile) apartment and find takeout bags from Gus Fring’s (Giancarlo Esposito) fast food restaurant, as well as a notebook with detailed instruction for meth production with an inscription “To W.W.” These leads are brought to Hank Schrader’s (Dean Norris) attention, and he then links Gale to Gus and suspects the fast food tycoon is actually involved in the drug ring.
Back at the White household, Skyler (Anna Gunn) monitors finances to conceal the illicit dealings occurring in her family. At work, she has to deal with her boss Ted Beneke (Christopher Cousins) concealing business revenue on tax returns, an act that could lead to an investigation into all of those involved. With a new threat to expose her family’s illegal money laundering, Skyler tries to convince Ted to pay off the difference, but his refusal puts Skyler’s family in danger.
Jesse Pinkman (Aaron Paul), once again sober, is taken under Mike Erhmantraut’s (Jonathan Banks) direction and given several tasks that boost his loyalty to Gus and the ring. The food trucks that deliver Gus’s meth products around the Southwest are being attacked, and he learns that member of the Mexican Cartel are behind them. He agrees to meet with them and brings Jesse along, who has also been instructed by Walt (Bryan Cranston) to poison Gus with a capsule of ricin. Jesse hesitates and doesn’t follow through with the act, but instead is entrusted to travel to Mexico with Gus to lead others in blue meth production.
A standoff in Mexico sees Gus confronting the head of the Cartel Don Eladio, with whom he has a longstanding rivalry. Gus poisons the members of the Cartel and manages to escape the country with Jesse and Mike by his side.
Back at the lab, Walt finds himself useless as Jesse’s loyalty to Gus strengthens. Walt is tasered and dragged out to the desert where Gus officially fires him and threatens danger if he reveals the operation to the DEA. Enraged and with the threat of his family’s safety at stake, Walt realizes the only way to save himself is to bring down Gus and his empire. However, he can’t do it without Jesse’s help.
In the meantime, Jesse learns that Andrea, his girlfriend, has rushed to the hospital after her son suddenly fell ill. Jesse thinks that the boy has been poisoned with the ricin originally intended for Gus, and Walt convinces Jesse that Gus’s accomplices were behind the scheme. Jesse uses this information and a regained trust for Walt to lure Gus to the hospital with the intent for Walt to plant a bomb on Gus’s car during the visit. The plan is futile, however, when Gus becomes suspicious and never returns to his car.
At this point, Walt realizes the only way to catch Gus off guard is during the drug boss’s visit to former Cartel leader, rival, and wheelchair-bound Hector Salamanca. Although Hector despises Walt for aiding the death of his nephew Tuco, he despises Gus as a business rival even more. Hector is ready to act as martyr when he detonates a bomb secured to his wheelchair when Gus is trapped in his nursing home room during a visit.
With Gus finally gone, Walt calls to his wife to announce that he has won. The season closes with a shot of a lily of the valley plant in Walt’s backyard, which he used to poison Andrea’s son in order to win back Jesse’s loyalty.