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 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 enemy? Who wiped her memory? And who is behind the tattoos?

The team unlocks a cryptic tattoo that points to Major Arthur Gibson, 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.

An infamous crew of thieves almost pulls off the perfect jewel heist, except one thief - with a Navy SEAL tattoo identical to Jane's - is captured at the scene of the crime. Does this man know Jane? Meanwhile, Jane receives a visit - and an ambiguous warning - from the mysterious bearded man from her first memory as Weller and Mayfair struggle with Jane's role on the team.

Jane reels from a series of massive revelations about her tattoos and grapples with whether to trust Oscar. Meanwhile, a tattoo leads the team to a shocking discovery in the Black Sea.

After a painting featuring one of Jane's tattoos is heisted from a gallery, the team discovers Jane is the real target. In order to protect her team, Jane goes AWOL.