A beautiful, naked amnesiac is found in Times Square covered in mysterious tattoos, including one bearing the name of FBI Agent Kurt Weller. Special Agent Weller and his team must decode the map of clues on Jane Doe's body in order to thwart a deadly terrorist attack.

The team unlocks a cryptic tattoo that points to an Air Force pilot with a painful past and a lethal agenda. Jane continues to search for clues to her identity and is haunted by flashes of a disturbing memory. Meanwhile, Weller thinks he might know Jane's true identity.

When an infamous crew of thieves almost pulls off the perfect jewel heist, one thief - with an identical Navy SEAL tattoo to Jane's - is captured at the scene of the crime. Meanwhile, Jane receives a visit, and an ambiguous warning, from the mysterious rugged man.

Patterson and her puzzle-expert boyfriend 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.

After a hostage situation turns out to have international implications, the CIA and FBI find themselves racing against each other to apprehend the criminal. Carter expresses concern about Jane's trustworthiness, causing friction with Mayfair and testing Reade's loyalty.

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