While in Cuba investigating about the tailfin, Ben and Vance get into trouble with the Cuban police and intelligence agency. As Michaela and Zeke travel to Costa Rica on their honeymoon, the former rescues Angelina from her religious parents who locked her up, believing she’s possessed.
As Michaela returns to work, she views footage of Jace, Pete and Kory coming out of the lake, whereupon she arrests Pete, while Jace and Kory flee. Tim Powell helps Ben to rescue Vance. Reporters swarm the Stones' house, as news spreads of finding a piece of Flight 828.
Upon a calling, Ben finds Eagan, an 828 passenger who helps him rescue a teenager. Olive examines an ancient Egyptian artwork of the goddess Maat in an attempt to help the passengers. A calling leads Michaela to Greg, whom she finds dead. Vance rejoins the National Security Agency.
Vance invites Ben and Saanvi to take a look at the latest information NSA gathered about Flight 828. During a calling, Zeke finds out that he’s having the same feelings and visions as Beverly. Jace shoots Kory for trying to stop him taking revenge on Coach Hannity.
Emmett kidnaps Jared, whom he gives a false account of Fitz’s death. While looking for Jace, Michaela finds a drawing that resembles part of the artwork on Maat. As Tarik spills the beans at a bar, a reporter overhears him and posts the family’s location online.
While confronting Jace, Michaela’s thrown off of a cliff and Jace sets out to find Cal, after which Zeke and Jared rescue her. As Jace attacks the family, set on killing Cal in order to escape death, a fatal confrontation ensues.
Owing to what happened, Dr. Gupta tells Saanvi and Ben that they’re off the Eureka projects as soon as they’re done with their ongoing tasks. Many 828 passengers receive a calling about the Eureka team. Gupta decides not to dismiss Saanvi, who unearths an important fact about the bodies.
Upon a calling, Michaela and Ben set out to help an 828 passenger. Saanvi analyzes the petrified wood that was found in the container, which she hypothesizes could be from Noah’s Ark.
While running experiments on the wood, Saanvi’s met with an unfortunate incident. As Jared starts seeing Sarah, Zeke’s certain they’re a perfect match. Ben, Michaela and Eagan get similar alarming callings.
As New York is hit by an earthquake, which Saanvi believes was caused by the petrified wood, she devises a plan to move it with Troy’s help. Ben crosses swords with an old foe, while trying to rescue his son with the help of Astrid, an 828 passenger, whereupon he gets arrested.
At court, the judge sets a huge bail for Ben's release, putting him on house arrest, which forces Grace to take action, ruining her own plans. Saanvi learns of new experiments being run on the tailfin, which she’s concerned will bring about far more tragic consequences.
As Cal experiences great pain as a result of Eureka’s ongoing experiments on the tailfin, Ben and Grace plead with Gupta to stop, but she’s deaf to their pleas, whereupon Cal disappears after touching the tailfin. Michaela strives to get to the bottom of a calling to prevent an imminent death.
Ben, Grace, Vance and Olive work together in an attempt to bring Cal back. To make amends for past sins, Saanvi embarks with Ben on a risky mission. Upon learning of Eagan’s holding Vance’s son hostage, Michaela, Zeke and Jared set out to stop him.