When Cal is discovered missing from his bedroom, Grace and Ben launch a desperate search which takes them to the remote mountains of upstate New York. A tantalizing trail of breadcrumbs leads them to a startling, game-changing discovery. Meanwhile, Michaela confronts the deceptive Autumn, and the shadowy "Major" finally makes an appearance.
Willing to follow any lead to keep his son safe from The Major, Ben heeds Cal's calling to help Captain Daly clear his name for what happened to Flight 828. The journey uncovers a seeming conspiracy that stems all the way back to the day the plane disappeared. Meanwhile, Michaela assists Autumn in her own journey of redemption.
Michaela's mystifying, next-level calling launches her on a mission that brings her relationship with Jared to a head. Determined to protect his family, Ben explores an alternate meaning to Michaela's calling that leads him to a new alliance and a powerful new adversary. Cal's struggle with Ben's absence from home forces the Stones into an agonizing confrontation that could alter the family's fabric forever.
Ben forms an unlikely partnership with Vance in a high-stakes race to locate the missing passengers of Flight 828. Meanwhile, Michaela helps a suicidal passenger who believes he is the Angel of Death, and Cal goes back to school, navigating both his unwanted celebrity and his former friends, who are all now 16 years old.
With the detained passengers secretly moved and subjected to painful experimentation - and Cal's health directly linked to them - Ben takes advantage of an old friend to find out where the passengers were taken. Meanwhile, a mysterious new version of the calling pulls Michaela into a murder investigation that has deep personal ramifications for her.
When Cal wakes with a life-threatening fever, Grace worries it's a side-effect of his experimental cancer treatment, but Michaela and Ben suspect Cal's condition may be related to a mysterious passenger from Flight 828. As Cal's situation worsens, Ben and Michaela attempt to track down the now-missing passenger.
The passengers from Flight 828 find themselves under government scrutiny as they struggle to resume their lives. Michaela is forced to confront the fact that Jared is married to her once-best friend, while Ben tries to help a fellow passenger reconnect with his son. Cal is approached by an obsessive stranger, as Grace and Olive disagree on whether or not to reveal a devastating secret.