The beginning of the second season hits the ground running as Walter White (Bryan Cranston) and Jesse Pinkman (Aaron Paul) are kidnapped by their new drug distributor Tuco after DEA raids Tuco’s Albuquerque operation.
The drug lord drags them out to home of his uncle Hector Salamanca, a former crime boss who suffered a stroke is now confined to a wheelchair. Walt and Jesse learn that Tuco plans to move them to Mexico to continue their business, but the two manage to escape before plans move ahead.
Tuco, on the other hand, isn’t so lucky and is shot down by Hank Schrader (Dean Norris) after an intense standoff between the drug lord and the DEA agent.
Walt returns home after disappearing for several days, and Skyler (Anna Gunn) becomes suspicious of his odd behavior.
Jesse takes his riches and rents a new apartment with drug money. He becomes romantically involved with landlord’s daughter Jane (Krysten Ritter), a recovering heroin addict.
When Walt and Jesse’s rapid business expansion causes distribution troubles and run-ins with the law, Walt hires criminal attorney Saul Goodman (Bob Odenkirk) to clean up the mess and protect their business.
Back on the crime-fighting front, Hank is rewarded for killing Tuco and is sent to El Paso, Texas for a promotion. What he doesn’t let on, though, is that the memories of the previous shootout send him into panic attacks. After witnessing the brutality of the crime scene in El Paso, including the beheading of a criminal and planned bombing of the DEA squad, he is sent back home to Albuquerque.
Gretchen, a former friend of Walt’s, discovers the chemist has been lying to his family that she has been helping pay for his medical bills. Confronted by Walt that she and her husband Eliot cheated him out of a business venture they started years prior, she keeps quiet about the money for the sake of protecting Walt’s family.
Also worried about the financial stability of the household, a very pregnant Skyler returns to work for her former boss Ted Beneke (Christopher Cousins) and begins to rely on him for emotional support as Walt’s double life takes a toll on their marriage.
As Walt’s cancer clears and the last of his products are sold into the hands of awaiting junkies, he soon finds normalcy boring. Jesse, on the other hand, continues to sell until one of his distributors and friends is shot by a competing drug ring. Distraught, he spirals into a drug-induced frenzy and brings Jane out of sobriety and down with him.
Word about the shooting gets out, and the pair’s distributors begin to back out to protect themselves. Unsure of what to do, Walt and Jesse turn to Saul and his uncanny connections with criminals to set them up with fast food restaurant-owner Gus Fring (Giancarlo Esposito). Discreet but incredibly successful, Gus brings the two huge expansion and a handsome salary boost. But in a test to see whether they were truly up for the job, Walt is sent on an impossible one-hour delivery on his own after finding Jesse incapacitated from a heroin injection.
Not only does this create a divide of distrust between Walt and Jesse, but Walt’s absence from his wife giving birth to their newborn daughter also causes troubles at home. After a fallout, Walt and Jesse agree to discontinue their partnership.
Walt ends up at a bar to drown his sorrows and coincidentally runs into Donald, Jane’s father. After a chat about helping their loved ones through difficult struggles, Walt returns to Jesse’s apartment to find him and Jane in another state of high from a heroin injection. A failed attempt to wake Jesse leaves Walt in the room when Jane is knocked onto her back and begins to choke on her own vomit. Walt hesitates to move her onto to her side but then leaves her to asphyxiate before leaving.
Jesse slumps into depression when he finds Jane’s dead body the next morning and believes himself to be responsible for her death. Walt brings Jesse to rehab, all the while Gus begins to unravel the truth that Walt has cancer and that his brother-in-law is Hank the DEA agent.
An increasingly suspicious Skyler also unravels information about Walt’s double life, which sees her leaving her husband out of fear and anger. After she leaves their shared Albuquerque home, Walt witnesses an explosion in the sky. We learn that the man Walt encountered days earlier, Donald, is an air traffic controller and, distressed after the death of his daughter Jane, accidentally guides two planes into each others’ courses.