The writers did not hold back in the penultimate episode of Blindspot’s first season. And with the fate of the Jane Doe Project hanging in the balance, the final minutes of the episode left more questions than answers.

The episode opened with a man in hospital scrubs carrying a duffel bag. Looking nervous, he dropped the duffel bag underneath a bench, before scurrying away. The bag was later found by a random passer-by, a small cry cluing in the audience that the contents of the bag contain a baby.

Meanwhile, Mayfair returned from jail, now under house arrest. Weller assisted her with the move, urging her to either take a plea or come clean about her more controversial actions earlier in the seasons. Mayfair refused both. She remained adamant that nobody would believe her when she claimed that Sophia was alive.

Back at government building, Weller continued to work on proving Mayfair’s innocence, which read as bittersweet in respect to the part he played in her arrest. His attempts were cut short, however, when Director Pellington approached Weller, criticizing his team’s fixation on a series of tattoos. He demanded that the Jane Doe Project be shut down.

In the office, Patterson informed the team of a recent event of interest: a small duffel bag found containing a baby. Disturbingly, a photo of the child revealed a barcode tattoo on its arm, matching another one of Jane’s. Noticing Pellington, Weller ordered Patterson to take the information off the screen, leading his team into another room.

Around the same time, a package arrived at Mayfair’s house, containing a photo of a man we believe to be Oscar. She placed the photo next to one she had of Angela, attempting to piece together her false arrest and Alexandra’s murder. Mayfair must’ve had a breakthrough, because she suddenly ripped off her ankle monitor, attaching it to her dog. She quickly and quietly slipped out of her home.

Out of the sight of Pellington, the team continued to work on the case. They concluded that the baby had quite a bit in common with Jane, from an unknown identity and origin to being found in a duffel bag. Patterson suddenly intercepted an email from the nurse who dropped off the baby, providing a time and location the team could find him. They set out.

At the site, Patterson called the team to inform them that the baby contained the same genetic material as Bryce Warren, son of the influential Peter Warren. They did not have much time to speculate, however, as the nurse they were chasing after was shot by an unknown source.

Following Patterson’s lead, the team went to Warren’s house. The lead turned out to be a dead end, however, when Warren remained adamant that he only had one child, a young boy with Leukemia. Investigations slowed to a halt when Peter Warren arrived on the scene, demanding to know why the team was there. Pellington took Jane off the team as punishment and restricted the rest to investigating the shooting, nothing more.

Meanwhile, Mayfair followed her own lead to a bar in town, finding Dennis, a man she had intercepted in a previous episode. While Dennis did not know the whereabouts of Sophia, he was able to point Mayfair to a cigarette store in town she often frequented.

As Jane left the office, Patterson discovered that Mrs. Warren was the infant’s biological mother. This discovery puzzled the team, as it seemed incredibly unlikely that Mrs. Warren was recently pregnant.

Exiting the building, Jane spotted a mysterious women breaking into the office, and followed her through. However, she was ambushed in the elevator before ever reaching her, forced to deal with her attackers first. The woman pushed her way through the building, shooting down anybody who got in her way, and exited with the baby.

At the cigarette store, the shopkeeper informed Mayfair that while he did not know the whereabouts of Sophia, that she did leave a number. Mayfair called Reade, requesting that he trace the number. While Reade agreed to do so, Zapata appeared nervous and afraid for both him and Mayfair. She warned him to be careful.

Unexpectedly, Mrs. Warren arrived at the government building. She admitted to Weller and his team that she and her husband were enrolled in a program on the verge of printing genetic material, which they needed to save their son. She and her husband had given the program their genetic samples about a year ago, with their son’s first transplant scheduled for the next day. Weller informed her of the haunting implications of the program: they were growing babies, not tissue. She gave Weller and address and the team headed out.

Instead of Reade, Tasha called Mayfair with the tracing information, urging Mayfair to not give up on her. Meanwhile, Jane arrived at the site of the program printing children.

The next moments in the episode unraveled quickly and brutally. Jane was discovered on the site by the mysterious women and the two viciously attack each other. During their struggle, the rest of the team arrived on the site and quickly took down the project. The FBI appeared shortly after, delivering the babies to Child Protective Services until their genetic matches could be found.

Furious at his insubordination, Pellington banned Jane from the government building for good, while promoting. Weller as a clever power play. Exiting the building, Weller finally confessed his feelings for Jane, kissing her goodbye. The happy moment was cut short, however, when Weller received a call informing him that his father was about to pass.

Watching her friends as she left, Jane once again followed her own lead to the address she discovered Weller at in the previous episode, putting her face to face with a vengeful Mayfair. Mistakingly believing that Jane was to blame for her arrest and Alexandra’s murder, Mayfair attacked Jane, only to be shot down by Oscar. Mayfair died believing that Jane was her persecutor.

As Weller’s father lay dying, he began to utter strange and disturbing riddles to his son. Two messages were spoken clearly: “She’s under the fort” and “I killed Taylor Shaw.” Weller looked at his father in horror as he realized the implications of his confession, Taylor Shaw being Jane Doe’s true name.