In this era, Raritan Laboratory is an army base. Four soldiers are sitting around playing cards, when suddenly they are splintered away without warning.
Railly continues to be haunted by visions of the Witness. She injects herself with her tether and splinters to 2044.
Jones and Eckland are in her bed, playing cards, when the alarm sounds.
Railly returns from 2016, continuing to see the Witness in her visions. She tells Jones and the rest of the team what she is seeing. She sees the Witness doing something to the time machine, then wakes up on the floor of her room. She speaks with Cole, who says he doesn't mind her friendship with Deacon. They agree that perhaps they don't know each other that well anymore.
Jones realizes a second, "phantom" tether entered the facility at the same time as Railly. The time machine malfunctions and is locked into permanent splinter mode. To prevent the machine from destroying the facility, Jones sends Deacon and Eckland to get a replacement lens for the time machine, while Cole and Railly try to shut down the power.
Suddenly, a horrifically deformed person appears and points a gun at Jones, before being shot down. Jones reveals that the man was once a test subject for Project: Splinter, and they deduce the machine is splintering people from random points in the timestream into the Temporal Facility.
Deacon and Eckland find the lens but run into two soldiers from 1959. When Deacon tells them they're in 2044, they start shooting. Initially, Eckland refuses to fight but ends up killing the soldiers with a grenade.
Jones says that the machine is breaking down and that anyone who tries to repair it will be exposed to lethal radiation. Eckland replaces the lens, sacrificing himself to save the facility in front of Jones's horrified eyes.
Cole loses track of Railly, and Ramse of Sam. Cole and Ramse run into each other and decide to go shut down the power. They see Railly with Sam. She locks herself and Sam into a room and points a gun at Sam's head. In a vision, she passes with Sam through the Red Forest and into the house on the hill, where a door is locked behind her, preventing her from escaping. She looks out a window and sees a water tower with the inscription "Titan," and the sigil of the Army of the 12 Monkeys.
Sam gestures to Ramse, who realizes that he is saying that an underground passage will allow them access to the room. Deacon arrives and helps Ramse get Cole into the room, despite the interference of two soldiers from 1959.
Cole realizes that the Witness is controlling Railly and manipulated her into sabotaging the time machine. He tries to reason with her, to no avail. Deacon tells Ramse he must get into the room and kill Railly to save Sam, since neither he himself nor Cole can do so. Once inside the room, Ramse points his gun at Railly. Cole has Ramse shoot him instead, saying the real Railly would never let him die. This allows her to break free of the Witness's control.
Ramse shuts down the power core, but a backlash of temporal energy strikes Sam and he splinters away. Ramse abandons Project Splinter and leaves on his own. Railly tends to Cole. Jones tells her the phantom tether was some kind of signal that allowed the Witness to control her. She gives Railly injections that will counter the effect of the red hallucinogen and prevent the Witness from influencing her mind. Jones says that Eckland's death and Sam's disappearance were both her fault, and resolves to set it right.
Sam finds himself in a forest where the red herb is growing. A hand is held out to him by a (unseen to the viewer) figure and he takes the hand and goes with them.