With Jane (Jaimie Alexander) in a state of near-constant panic over her identity, Dr. Borden (Ukweli Roach) administers a Rorschach test. But all Jane's got is the memory of weapons training in the woods with the ruggedly handsome man. Meanwhile, Weller (Sullivan Stapleton) has breakfast with his sister Sarah and her son Sawyer, who have moved in while looking for an apartment. Sarah mentions their father called to ask if they're attending Taylor's yearly memorial? Weller is definitely not interested. At work, he tells Patterson (Ashley Johnson) that he noticed a scar on the back of Jane's neck. Then he runs Jane through more weapons training, hoping to trigger another memory. One thing's for sure: Jane knows her guns, and she now remembers shooting a nun in the back of the head. Stunned, she refrains from telling Weller, just as word arrives that Chao is dead of a massive stroke. Surveillance footage shows a man walking away from Chao's room as everyone else rushes toward it... Suddenly, Patterson announces that she's decoded a Vigenère cipher on Jane's neck: Maj. Arthur Gibson - a Silver Star-awarded pilot, who once injured, left a desk job in Nevada to work for the Air Force in New York. Convinced Gibson may know something about her, Jane insists on accompanying the team to his home in Brooklyn. Refusing to talk, Gibson orders the team off his property. As they head back to their SUV, Gibson's house explodes.  The only thing that survives the explosion is a wall safe - no sign of Gibson. The team questions Air Force Colonel Margaret Powers, who explains that after experiencing collateral damage on a mission, Gibson's increasing paranoia and PTSD earned him a desk job and, ultimately, a discharge. But after reviewing Gibson's files, Patterson finds that not only did the Air Force not fire Gibson, they promoted him - and gave him top security clearance. Weller figures the Air Force made Gibson a drone pilot, which means there must be a drone program in New York. Meanwhile, Gibson kidnaps Emily, the six-year-old daughter of his co-worker Alex, in order to force his assistance in launching an armed drone. Moments later, the drone drops a missile on Colonel Powers as she's getting into her SUV. Frustrated, Reade (Rob Brown) wonders whether Jane and her tattoos are to blame. Weller insists it's not Jane's fault; they need to focus on finding Gibson.  Furious, Mayfair (Marianne Jean-Baptiste) calls General Fitzmorris, who admits Gibson worked for a secret domestic drone surveillance program, and the drone he now controls is armed with two more missiles. Distraught over the general's disregard for Emily's welfare, Weller blows up, so Mayfair orders him to stand down. While Reade speculates that whoever tattooed Jane knew about the drone program, Jane flashes back to shooting the nun. Maybe her tattoos are some kind of penance? Mayfair pulls Weller aside, to chastise him for yelling at Fitzmorris. Weller admits he's been thinking about Taylor, who went missing 25 years ago when he was 10. In his last memory of her, Taylor fell while climbing a tree, leaving a scar on the back of her neck - the same scar as Jane's. Weller knows why his name is on Jane's back: Jane Doe is Taylor Shaw.  Paterson cracks Gibson's safe, finding an air-gapped laptop with a list of five seemingly unrelated domestic accidents - yet the victims of each incident were all from the Middle East. Gibson's initials are associated with three, the initials I.M. with the other two. Patterson thinks I.M. is Major Ivon Musgrave, so the team scrambles to his Brooklyn apartment. When Musgrave runs, Jane gives chase. An intense fight ensues, until Weller intervenes, hauling Musgrave onto the street. Musgrave demands to talk to Colonel Powers, just as Jane spies the man from her memory. That's when the second missile hits, blowing the team back into the apartment building. Jane rushes to help an injured Reade, then stumbles back to the street, but the man from her flashback is gone. Back at HQ, Musgrave explains that Gibson wanted to expose the drone program, which was rife with collateral damage. When he asked for help, Musgrave turned him in, then helped the Air Force destroy Gibson's life. Since Gibson has one missile left and is dead set on destroying the program, Weller asks Fitzmorris where the drone pilots work from... and it's the top three floors of the building they're in. Twice a day, every pilot is in the building for a shift change, which is in one hour.  As the building evacuation begins, Patterson narrows Gibson's location to one of two construction sites in Brooklyn. On the way, Jane tells Weller that she did remember something... what if she's a terrible person? Insisting Jane has a good heart, Weller leaves her in the car, then runs to check the roof. After a firefight, Gibson takes the elevator down as Weller tries and fails to warn Jane. Gibson open fires on the SUV, then drives off, so Jane decides to follow, forcing a crash and rolling her own car, which brings on another flashback. The nun is actually a soldier in disguise. After the shooting, Jane pulls a coded USB fob from around his neck. After pulling a woozy Jane out of the SUV, Weller extracts Emily's location from Gibson and returns the little girl to her father.  Back at HQ, the team argues about the day's events. The Air Force has already come up with a cover story for the press, and Reade isn't convinced Jane's tattoo saved thousands of lives. Mayfair pulls Weller aside to advise that Patterson is running DNA tests to confirm whether Jane truly is Taylor. But Weller doesn't need test results - even if he's not ready to tell Jane. That night, he runs his theory by his sister. Stunned, Sarah reviews how this could change all their lives: their father was accused of kidnapping and killing Taylor, causing their mother to leave. Weller has spent the last 25 years believing his father murdered Taylor... and now their father is dying of pancreatic cancer. Soon. Across town, Jane is surveying the dismal contents of her safe house refrigerator when someone grabs her from behind... the ruggedly handsome man.
While a tattoo sends the team after a drone pilot gone crazy, Weller seeks to confirm that Jane Doe is a missing person from his childhood.