Most of the season follows two different timelines. The primary timeline begins with Ellen Parsons' recruitment by Patty Hewes to "Hewes & Associates" and follows proceedings of a class action lawsuit against Arthur Frobisher by his former employees, whom Patty represents. The initial episodes follow Patty's attempts to capture potential witness Gregory Malina through Katie Connor. The arc further details Malina's involvement with Frobisher's lawyer Ray Fiske and the pressure Patty brings to bear on Fiske on Malina's subsequent death. The narrative includes multiple flashforwards of the alternative timeline, set approximately six months after Ellen's appointment, until both timelines converge in the penultimate episode of the season. The alternative timeline details the attack on Ellen, her arrest for the murder of her fiancé David Connor, and the subsequent murder investigation.

The second season, like the first, follows two different timelines. The primary timeline follows Patty, Ellen, and Tom as the firm goes up against an energy company who have engaged in unethical practices. A former lover of Patty's, Daniel Purcell, brings the matter to her attention, but then inexplicably backs out, leaving Patty up against UNR CEO Walter Kendrick and his fierce lawyer Claire Maddox. Meanwhile, Ellen works with the FBI to bring down Patty, while also seeking revenge on Arthur Frobisher for his presumed role in her fiance's death. Ellen is unaware that Patty is suspicious of her, and that Frobisher's criminal connections appear to extend to her new friend Wes. A second timeline takes place six months later, when Ellen meets with an unknown person in a hotel room, and subsequently appears to shoot them.

Set a year after season two, Patty's focus now rests on Louis Tobin, the patriarch of a wealthy family, who has just confessed to orchestrating the largest Ponzi scheme in Wall Street history. The government has tasked Hewes and Shayes with finding the Tobins' hidden money and uncovering any evidence that other family members had knowledge of the fraud. Ellen Parsons has taken a job at the New York District Attorney's office, but she finds herself being pulled further and further back into Patty's orbit. Tom, who had invested with Tobin, has lost 70% of his net worth, as have numerous others he helped invest. He struggles to keep his involvement from interfering with the case and secret from Patty.

The fourth season takes place two years after the Tobin case. Ellen has moved on with her life. Now an attorney at her old mentor's firm, she's content with her cases and colleagues. Deep down, however, she wants a bigger challenge. When she discovers her friend has been through a traumatic experience while working for High Star, a private security firm hired by the U.S. government to carry out special missions in Afghanistan, she suspects foul play and asks Patty for help. Patty knows that trying a case against High Star can make Ellen's career. Or ruin it. It was inspired by recent events and controversies surrounding Blackwater Security Consulting.

In the final season of Damages, Patty and Ellen are pitted against one another in two separate cases. The first involves a wrongful-death suit brought against Channing McClaren, the founder of a whistleblowing web site, who's implicated in the death of a trader for an investment firm. In the other case, Ellen is called as a witness to testify against Patty in the custody battle with Patty's son, Michael.