Season 2 kicks off with Walt and Jesse once again bearing witness to Tuco's incendiary disposition, which leads them to the conclusion that it's time to put an end to their business dealings with him. But the question is how. Meanwhile, Hank serves as a go-between for estranged sisters Skyler and Marie.
Trying to dissociate themselves from the volatile Tuco (Raymond Cruz) takes a bad turn when Walt and Jesse get trapped with the dealer, and Skyler, worried about her missing husband, receives comfort from her sister and brother-in-law. Hank, meanwhile, pays a business call on Jesse's mother (Tess Harper).
Walt and Jesse attempt to cover their tracks and distance themselves from Tuco, but they soon find that business is taking a hit along with their financial situation. Meanwhile, Hank and his DEA investigation into the meth ring get a major break that just might put Walt and Jesse in their crosshairs.
Despite Walt's attempt to reconnect with the family, a suspicious Skyler keeps him at arm's length and worries about what he's been up to while he's been away from the house; Jesse finds himself on the streets once again and struggles to improve his lot in life.
Hank deals with some lingering aftereffects from his confrontation with Tuco; bills are piling up at the White house and tensions are beginning to run high; Jesse organizes a crew of dealers to take their product to the streets.
Walt returns to teaching at the high school; when Skinny Pete gets taken advantage of and ripped off, Jesse steps in, but bites off more than he can chew; Skyler takes the opportunity to show her appreciation for Gretchen's kindness in picking up the tab for Walt's treatments.
Walt and Jesse contemplate an expansion of their business; Hank experiences a hassle in El Paso as he tries to adapt to his new coworkers; Skyler's new job opportunity leads to her reconnecting with an ex-colleague; and Jesse interacts with his new landlady.
Badger's brush with the law leads Walt and Jesse to call in a shady lawyer (Bob Odenkirk); the DEA believes it has a line on the mysterious and elusive "Heisenberg"; Hank's stint in El Paso is up and he returns to Albuquerque, but his mental makeup causes concern for Marie.
After undergoing a PET-CAT scan and fearing the worst, Walt takes lawyer Saul's advice and hunkers down for a marathon session of cooking product; Jesse's romance with his landlady is heating up, but must cool off quickly when he and Walt head for the desert to take care of business.
The Whites throw a party to thank family and friends for their support through Walt's trying time, but it turns ugly when he and Hank get into a bitter argument; later, a pent-up and fed-up Walt tries to occupy his time with home-improvement projects. Worried about Walt's physical and emotional states, Skyler confides in her boss; Jane keeps her relationship with Jesse a secret from her father.
Saul (Bob Odenkirk) suggests a new business partner for Walt and Jesse after they begin to lose their dealers to some unforeseen circumstances. At work, Skyler confronts Ted after she uncovers some unnerving information; and Jesse opens up to Jane about what he does for a living, with disastrous results.
A new addition joins the White family as Walter Jr. attempts to help out his struggling family by launching a new Web site. Elsewhere, Jesse's addiction worsens and his relationship with Jane begins to negatively impact Walt and her father (John de Lancie).
In the Season 2 finale, Skyler's frustration with Walt's secrecy boils over; Jesse is dealt a devastating blow that leads him down a path of self-destruction, and only Walt is willing to help him; and a grief-stricken Donald experiences more tragedy.