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.
Patterson and her puzzle-expert boyfriend, David, 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. Carter 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. Jane and Weller attempt to keep their relationship professional. Zapata struggles with a moral issue.
One of Jane's tattoos sends the team to a remote location where they find themselves face to face with a dangerous criminal in a case that puts Jane and Weller's strained relationship to the test and threatens to expose Mayfair's secrets. Meanwhile, Patterson breaks the rules to solve a tattoo puzzle.
After a police officer is murdered, Patterson unlocks a disturbing tattoo that appears to have predicted his killing, and the team chases a violent clue trail to stop further attacks. Mayfair reveals secrets from her past to Weller, seriously testing their relationship.
Jane and Weller go undercover as a world-class assassin couple to prevent deadly information from getting into the wrong hands. The intimate assignment draws them closer than ever. Meanwhile, David embarks on a solo mission to win Patterson back, and Carter clashes with Mayfair over how to handle a dangerous individual.
In the thrilling mid-season finale the team goes after a group of sleeper spies that have just been activated and race to stop a slew of assassinations.
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 disturbed Iraq War vet shoots up a military base, the team exposes a sinister plot. As Jane and Weller race to stop a single-minded scientist, Jane recalls her own mysterious military past and contemplates a new relationship with Oscar.
After a tip reveals there's a mole within the FBI's New York Office, the team must hunt for the operative while facing extreme scrutiny from Inspector Fischer. The team's deepest secrets threaten to be exposed, and everyone is a potential suspect - but some, especially Jane Doe have more to hide.
An anonymous tip leads the team to investigate an urgent death row case, ultimately sending Zapata undercover. After nearly getting caught during the mole hunt, Jane considers leaving the FBI.
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.
After an armored truck is robbed, the team discovers that the stolen goods are chemical weapons and they must race to thwart a terrorist plot. Meanwhile, Jane grapples with a confusing memory of Weller - while growing even closer to Oscar. Meanwhile Patterson receives a phone call from someone from her past.
After Patterson discovers a hidden message in the New York Times crossword, she embarks on a tattoo scavenger hunt that leads her into danger. Oscar finally tells Jane more about who she was, and Weller seeks his Dad's opinion about who kidnapped Taylor Shaw.
In order to capture a dangerous international criminal, Jane and Weller are forced to collaborate with the only person he will meet: their former target, Rich DotCom. Jane must decide whether to risk hurting Weller by executing a morally questionable order from Oscar.
When a school shooting breaks out during the investigation of a tattoo, the team splits up to take down the shooter. Mayfair copes with some issues from her past.
When a mysterious young girl with a tattoo connection falls into Borden's care, he brings her case to the FBI team -- but her ties to a terrorist organization prove dangerous for all of them. Meanwhile, a conflicted Jane starts to grow close to Weller again, and friendship blossoms between Borden and Patterson.
The FBI is locked down when criminal hackers infiltrate the building, trapping the team inside SIOC. As they fight their way out, the close quarters force Mayfair, Zapata, Reade, and Sarah to confront personal conflicts.
After an abandoned baby is found with a tattoo identical to one of Jane's, the team races to piece together the child's identity and save dozens of infants. A furious Jane confronts Oscar about the outcome of his secret missions.
Weller searches for the truth within a heartbreaking and confounding assertion. Jane reaches out to a former suspect for help with Oscar. Meanwhile, the rest of the team struggles to help a friend...