Season three sees tension in the White household mounting. When Walter White (Bryan Cranston) tells Skyler (Anna Gunn) about his business dealings, she follows up with divorce papers that Walt refuses to sign. Instead, he continues his business and joins forces with Gus Fring (Giancarlo Esposito), working in his super lab with new assistant Gale Boetticher (David Costabile). Skyler must protect the family and calls on Saul Goodman (Bob Odenkirk) to find a business cover-up to funnel Walt’s drug money into.
Back in El Paso, Hank Schrader (Dean Norris) becomes obsessed with tracking down the Heisenberg case and eventually links Jesse to the blue crystal meth production. Walt learns of Hank’s intentions to arrest Jesse. To help out Jesse, Walt warns him to destroy the RV they originally cooked in and get rid of any incriminating evidence Hank might uncover. He soon decides that he needs Jesse back under his wing and feigns disapproval of Gale to have his former partner reinstated.
Meanwhile, two assassins from the Cartel arrive in Albuquerque to avenge the death of their cousin, Tuco, under direction from former crime boss and now wheelchair-ridden Hector Salamanca. Although they originally go after Walt as the evasive Heisenberg, Gus meets with them and tells them that Walt is not the culprit, but the true murderer of Tuco was in fact Hank.
They attack the DEA agent, but he doesn’t go down without a fight when he kills one and severely injures the other. The showdown doesn’t go without losses of his own, and Hank is left paralyzed from the waist down from a gunshot wound.
Gus manages to take advantage of the investigations into Hank’s attackers and uses the opportunity to kill Cartel leader Juan Bolsa. This gives him complete monopolistic control over the meth business in the Southwest and Mexico.
With the boost in business, he gives Walt a larger cut of the profit but skims over Jesse, who he feels is a weak link in the business. To make up for it, Jesse steals away some of their daily production to sell on his own, including to recovering addicts he finds at a local rehab group. Here, he meets and begins seeing Andrea, who herself has complicated ties to the drug ring.
To assert his control over the business, Gus gets rid of Jesse and brings Gale back to the lab. Walt realizes that Gus has brought Gale back in as a replacement once Walt’s usefulness has expired. To prevent Gus killing him off, Walt pleads for Jesse to kill Gale to save both of their lives. A tense standoff between Walt and Mike Ehrmantraut (Jonathan Banks), Gus’s “cleaner,” leaves him with dwindling time to protect himself. He makes a desperate call to Jesse, who flees to kill Gale in his apartment.