In the series premiere, the discovery of Jane Doe sets off a vast and complex mystery that immediately ignites the attention of the FBI, who follow the road map on her body into a larger conspiracy of crime, while bringing her closer to discovering the truth about her missing identity. Special Agent Weller and his FBI team must decode the map of clues on Jane Doe's body in order to thwart a deadly terrorist attack. Who is Jane Doe — is she an asset or an enemy? Who erased her memory? And who is behind the cryptic tattoos?

A hidden message on Jane's body reveals a plot that could result in catastrophic consequences all over the world.

After a seemingly straightforward hostage situation turns out to have deeper international implications, the CIA and FBI find themselves racing against each other to apprehend the same criminal with a dark history. Tom Carter (recurring guest star Michael Gaston) expresses concern about Jane's trustworthiness, causing friction with Mayfair and testing Reade's loyalty to the team. Meeting Weller's family proves overwhelming for Jane as she grapples with her identity.

When an assassination leads the team to a dangerous app that allows criminals to track government vehicles, they have to work with the app's surprising creator to take it down. While Zapata struggles with a moral issue, Jane and Weller attempt to keep their relationship professional.