Season 1 ends with Lizzie racing to Boston, where Emma is taking refuge in the luxurious home of Adele Trotwood and her family, and being stunned to find a vastly different Emma than the cherished sister she knew. Lizzie unwittingly leads Bat Masterson and Tom Horn directly into their path; and Emma tries to ease tensions and makes an impetuous sacrifice.
Lizzie remakes herself as a school teacher with a new name in a town far from Fall River to be near Emma who is in an asylum. Meanwhile, two gunslingers, Bat Masterson and Tom Horn, hunt for Lizzie and want to know the fate of their friend Siringo. When Lizzie helps a victimized student get justice Lizzie-style, she jeopardizes her cover; and Emma makes a startling choice that leaves Lizzie devastated.
Lizzie devises a strategy that stops Siringo cold, and unleashes a more blunt and sinister side then ever before. Meanwhile, Emma begins to lose trust in Lizzie; and a co-conspirator who fails Lizzie realizes his mistake too late.
Siringo and Fall River's marshal strong-arm Skipjack to help lock tight the case against Lizzie. But Lizzie exerts her own brand of influence on a witness. Meanwhile, Emma reveals to Lizzie that a man in her life may change their relationship forever; and a woman in Siringo's life becomes tempting forbidden fruit.
Charles Siringo and Nance O'Keefe join forces against Lizzie; Skipjack, the new underworld boss, exploits a lethal secret Lizzie wants hidden; a haughty neighbor incites Lizzie's wrath by mistreating her dog; and a romance threatens to come between Lizzie and her sister.
Lizzie hosts a housewarming party in her new mansion, but the lavish affair is upstaged by a pesky actress who is distressed about her missing brother. He was last seen with Lizzie. Meanwhile, Mr. Flowers involves Lizzie in an extortion scheme; and Charles Siringo meets his anonymous employer who is determined to find the truth about Lizzie.
Lizzie and Emma visit New York City, where Lizzie saves a street prostitute from a violent beating. But her good deed is met with wrath from a local gangster. Meanwhile, a playwright tries to get Lizzie to finance his latest work; and Siringo turns up evidence that further incriminates Lizzie.
The life of suspected killer Lizzie Borden is explored, following her acquittal for her parents' murders. In the opener, Lizzie tries to restart her life, but a Texas Pinkerton agent shows up determined to learn the truth about the murders, and her father's ex-business partner demands a huge debt be paid.