Season two consists of twenty-two episodes; it follows Alex Parrish (Priyanka Chopra), who has been working undercover for the FBI as a CIA recruit to uncover a rogue faction called the AIC.

In the future, the President of the United States, the First Lady and several other world leaders are being held hostage at the G-20 summit in New York City by a group of terrorists called the Citizens Liberation Front.

After the collaborators gain access to the sensitive intelligence, Alex is reinstated as an FBI agent and is hired as a member of the task force along with Ryan Booth, Nimah Amin, Shelby Wyatt and Dayana Mampasi, and the leader of the group, Clay Haas, a renowned political advisory strategist.

As the season progresses, Henry Roarke, the Speaker of the House, is appointed as the president of the United States, replacing Claire after a national scandal.

Alex resorts to a final strategy: she publicly broadcasts Roarke's recordings with the Federal Security Service and emails the evidence to the ACLU and other rights organizations.

Due to Alex committing treason by releasing classified U.S. intelligence to the public at the Constitutional Convention, she is branded as a fugitive and an Interpol Red Notice for her arrest is issued.

[37] In late July 2016, Henry Czerny, who played the CIA director Matthew Keyes in the season 1 finale, joined the cast in a recurring role.

[46][47] Jasef Wisener of TVOvermind gave the premiere episode a rating of three and a half star, writing that it set up its sophomore season "effectively".

[48] Negative reactions included Allison Nichols of TV Fanatic, who was critical of the opening episode owing to the "confusing time jumps" and the "head-spinning plotlines".

[49] The episodes following the winter finale when the show's narrative switched to a single timeline garnered further praise by such critics as Madison Vain of the Entertainment Weekly and Kelsey McKinney of the New York Magazine, especially for its focus on character development.

"[51] In a full five-stars review of the sixteenth episode, McKinney wrote, "the show is grappling more and more with the emotions that make us all human, not just the ones that drive the story forward".