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?

The team unlocks a cryptic tattoo that points to Major Arthur Gibson (guest star Robert Eli), an Air Force pilot with a painful past and a lethal agenda. Jane continues to search for clues to her identity and is haunted when flashes of a disturbing memory force her to question her past. Meanwhile, Weller thinks he might know Jane's true identity.

After a run-in with the mysterious bearded man, Jane's SEAL tattoo leads to a violent gang of thieves - can they tell her who she is?

Patterson (series star Ashley Johnsone) and her puzzle-expert boyfriend, David (guest star Joe Dinicol) decode a tattoo clue that sends the team to the Centers for Disease Control (CDC). While at the CDC, the team discovers a hidden message on Jane’s body that uncovers a plot that could have catastrophic global consequences. Meanwhile, Jane and Weller grow closer.

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.