Tuco drives back into the junk yard and throws the body of No-Doze out of the car demanding that Walt do something. But there is nothing to do and No-Doze dies and is left to rot under a car by Gonzo. Jesse and Walt are terrified that they will now be killed and Jesse buys a gun. Walt suggests that they use ricin to poison Tuco. Marie is avoiding therapy and Hank asks Skyler to talk to her. Just as Walt seems ready to confess to Skyler, Jesse arrives with Tuco in the backseat of his car with a gun.

Tuco takes Walt and Jesse out to his place in the country where his disabled uncle Tio lives. He tells them that his operation was hit by the DEA and he suspects Gonzo may have tipped them off. He wants to take them to Mexico to cook in a Super Lab. They attempt to poison him with the ricin but Tio sabotages them. His warnings (with the use of a bell) lead Tuco to try and kill Jesse but they manage to shoot him in the stomach and leave him for dead. Meanwhile Skyler begins the search for Walt and Hank takes time off work to help. He follows Jesse’s car out to Tuco’s place and finds a wounded Tuco standing by Jesse’s car.

Walt and Jesse walk out of the desert and head home. Walt strips off in a convenience store and pretends that he can’t remember the last two days. Jesse clears the cooking equipment out of his house and pays Wendy to say he spent three days with her. Hank is welcomed home as a conquering hero and interrogates Jesse. Walt tells the hospital psychiatrist a version of the truth to be allowed out of hospital but has to break out and rush home when he remembers the nappy box with the gun and money in it.

Walt tries to get back in Skyler and Junior’s good graces by making breakfast and being attentive. Skyler isn’t buying it though and keeps disappearing with no explanation. Jesse’s parents kick him out of his house and he can’t find anywhere to stay. He ends up sleeping in the RV and then breaking out of Clovis’ yard.

Walt’s medical bills pile up and Jesse finds a new apartment. To pay for all of this they cook a new batch and Jesse recruits his friends to deal for him. Skinny Pete gets robbed by two addicts and Walt suggests that Jesse “handle” the situation. Meanwhile Hank receives a promotion before suffering post-traumatic stress from his encounter with Tuco.

Jesse heads to the house of Spooge and his partner but finds only their young son waiting there. He threatens them while trying to protect the kid from seeing anything damaging. Gretchen calls to see how Walt is and Skyler thanks her sincerely for paying for his treatment. Gretchen is taken aback but doesn’t give the game away. Walt goes to see her and blames her for cutting him out of “Gray Matter.”

Hank struggles at his new job. He doesn’t understand the language or the culture of compromise. Jesse is now a feared man in Albuquerque since it’s assumed that he did in Spooge. Walt decides that they should now expand and raise their price. Skyler applies for a job at her old workplace and her former boss Ted Beneke welcomes her back.

Badger is arrested for selling meth. He calls Saul Goodman to represent him, a local lawyer known for his cheap looking commercials. Hank returns to work in Albuquerque after a pep talk from Walt and is quickly on Badger’s case. Walt plays the part of Badger’s uncle and tries to bribe Saul when he fears that Badger will talk to the DEA. Saul refuses and so Walt and Jesse kidnap him. He outwits them, offers to represent them and finds someone else to take the fall for Badger.

Walt has a scan to see how his cancer has responded to the chemotherapy. Between a large mark on the scan and his coughing fits, he assumes he doesn’t have much longer to live. He tells Skyler he is flying out to visit his mother but instead he drags Jesse out to the desert to cook a huge batch of meth. Jesse leaves the key in the ignition and after two days of cooking the battery is flat. Their attempts to restart it fail and they are so far away that Skinny Pete can’t find them. Jesse inspires Walt to create another battery and when they return Walt’s diagnosis is good.

At a party to celebrate Walt’s good news the tequila is flowing. Walt lets Jr drink some as he gets annoyed by the way Hank plays surrogate Dad. Soon Walt looks into home repair and buys a new boiler before turning to the rot under the house. Skyler begins flirting with Ted Beneke at work. Jesse is falling for Jane and is annoyed when her Dad arrives and she blows him off.

Combo is killed after setting up shop in another dealer's territory. Jesse is upset and turns to drugs. Jane joins him and soon escalates things to heroin. Saul tells Walt to get out of the dealing game and sell his product to a local distributor who keeps a low profile. Walt goes to meet him but no one shows up. He then hears that the man doesn't want to business with Walt. So Walt returns to the Chicken restaurant where the meeting was to be held and talks to the manager.

Walt arrives late and meets his daughter Holly. Jane makes excuses to her father about missing her NA meeting while Jesse freaks out that the meth has been stolen. Walt refuses to hand over money to Jesse while he is using. Walter Jr sets up a website asking for donations to save his Dad and Saul suggests they funnel his money through it. Jane's father Donald barges in to find her using and demands that she go to rehab. She begs for one more day and she uses it to blackmail Walt into handing over the money. Walt does but then receives wise words from Donald in a bar.

Saul sends a man to clean up Jesse's apartment and prepare him for the arrival of paramedics. Once Jane is taken away Jesse flees to a crack den where he weeps in Walt's arms. Walt sends him to a health resort while he prepares for his operation. While under drugs to relax him he admits to owning two cell phones. Weeks later and Walt is ready to begin a normal schedule again and Donald heads back to his job as an air traffic controller. Skyler tells Walt that he has the weekend to move out. While he was recuperating she uncovered all his lies and wants nothing to do with him. Donald makes mistakes which lead to the collision of two planes over Albuquerque.