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In 2043, Jones realizes that the recording they've had of Dr. Railly has said "Army of the 12 Monkeys" and realizes that the symbol appeared in a mental institution in 2015. So she sends Cole and Ramsey to investigate. What Cole finds is room 248, where the symbol DOES, in fact, exist, but the file for the person in that room is missing. When scavengers attack them, they kill them and go back to the underground world where they live.
Back in 2015, Cassie asks Aaron for help and takes him to her grandparent's old bookstore. She lets him in on the strange occurrences with the police and The Markridge Group. He tells her she shouldn't be hanging around with a person who kidnapped her. Back in the future, Jones and Cole argue whether sending him back is really in the cards. Jones tells Cole not to see Cassie again, because he could destroy the entire timeline of the events.
When Cole enters the apparatus that sends him back in time, something goes wrong and he finds himself in North Korea in 2006. Jones and her team work furiously to get him back, and he's slapped around and questioned as a spy before he disappears and is sent to 2015, where he's confined to the mental hospital where Jennifer Goines, daughter of Leland, is kept. Cole figures that Jennifer must have some connection to the Army of the 12 Monkeys because, well, she's Leland Goines daughter and he was all wrapped up in this virus stuff. Meanwhile, Cassie can't get a hold of Jeremy, her NSA contact and sees that the Markridge Group is spinning Goines' death as a heart attack.
In the mental institution, Cole meets Jennifer Goines and when he asks her about the Army of the 12 Monkeys, she says that the monkeys live in her head and tell her to hurt people. She's been told not to talk about monkeys, and she finally escapes the conversation by calling security, who drag him away. When the doctor questions about it later, Jennifer mentions "the night room." This worries the doctor who calls people at the Markridge Group to tell them. They wire him more money. This thing goes deep, team.
When Cassie stops by Jeremy's house to get information, she finds him dead and covered in flower petals. Shortly thereafter, a terrifying old man threatens her and tells her to stop asking questions. He is really scary and Cassie doesn't really have a choice. When she gets back to her house, she chats with Aaron, who shows her CIA photos of Cole from 2006 in North Korea. This leads her to the J.D. Peoples Mental Institution.
At the Institution, Jennifer sneaks into Cole's room and tells him the truth about her past. That while she was working at Markridge, she heard voices in her head, on serious medication, and one night – the lab was raided by people wearing black outfits. They murdered her colleagues, asked about "the night room" and then framed her for the murder. It turned out that one of her colleagues escaped. But who was it? When Jennifer is discovered and Cole is being led away, Dr. Cassie Railly shows up and rescues him. As Cole tries to take Cassie to see Jennifer, they are thwarted by the appearance of that mysterious old man, who has kidnapped Jennifer. Cole learns that the scar on the old man's face was from him, Jennifer stabs the old man in the arm, and there's a fight in the boiler room that ends when the old man gets away with Jennifer.
Before he splinters back to the future, Cole has a lovely moment with Cassie and the two agree to team up together. And then, back in the future, Jones has a hard time accepting that. Meanwhile, that spooky old guy in the hat is giving a drugged potion to Jennifer as someone comes out of the shadows. Just. More. Creepy.
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