This episode begins in 2043, with Jones listening to a recording of Cassandra's, in which she talks about the plague starting with Leeland and when she gets to the part about the true architects, Cassandra brings up the army of the 12 Monkeys. Jones finds the image Jennifer drew in a mental institution back in 2015 of a monkey and decides to send Cole and Ramse to investigate.
In 2043, Ramse and Cole make their way through a parking lot at night. Cole heads in against Ramse's warning about a potential ambush. The two men make their way through a building by flashlight and enter room 249 to find a drawing on the room. Ramse feels that this doesn't make any sense because the recording says that Leeland is responsible. Ramse questions if Leeland is in fact dead. Cole confirms Leeland's death and adds that the recording said that the plague started with Leeland. Ramse questions if Cole wants to return to the past because Jones originally said that "this is one and done," but Cole now believes that Jones was wrong. After going through files, Cole notes that the file on 248 is missing and that it's the only one that's gone. ( it's worth noting that the director made a mistake here, unless there is some meaning here I am missing. The men entered room 249 but are talking about room 248.) Suddenly, Ramse and Cole are attacked but manage to get the upperhand on their opponents quickly.
Cole and Ramse enter return to the science lab and Ramse tells Cole that he is not the same man since he got back. Cole denies that this is the case but Ramse responds that he understands that Cole is sad since he's been back, adding that anyone would be. Ramse brings up that Cole had access to food, sights and yes, the girl but Cole assures him that it's not like that. Ramse reminds Cole that he's not from there but here. They then discuss whether or not Cole is going to see Cassandra again.
It's now 2015 in Washington D.C., and Cassandra calls Aaron for help. When Aaron arrives, Cassandra thanks him for coming and admits that she didn't have anyone else to call, as he drives through the city. Cassandra directs Aaron to take her to her grandparents old store because she wants to lay low for a little while. It's not long before a disagreement happens between them about Cole. When Aaron says that he wants to help, Cassandra suggests that he question why there were no charges laid against her, why she was released to the security firm to begin with, and particularly why they never made it the police station.
In the future, Jones says that the symbol (read: 12 monkey symbol) appeared in all of the major cities, adding that there was a design to ensure that the virus hit with maximum impact. Cole questions if the guiding hand was the army of the 12 monkeys. Jones says it's not clear yet who the 12 monkeys were and that they could have been a terrorist organization, or even religious fanatics. Cole wonders if he should go to 1987 to see Leeland but Jones says that they don't yet have enough power to send him that far back. Instead, pointing to a picture of Jennifer, Jones says that they are sending him back to 2015 to track her down because she is somehow connected to the 12 monkeys. Cole suggests that Cassandra would be great at helping him get inside the institution but Jones does not want Cassandra to become Cole's accomplice. Cole reminds Jones that she wasn't there and Jones points out that Cole could have corrupted Cassandra's timeline and prevented her from leaving the message which would have stopped their entire investigation. Jones suggests that Cole is risking everything by playing with time, adding that she has learned enough about time to fear it.
Cole is given an injection and Ramse tells Cole that he wants him to do a shot, get laid and find some vintage. Cole jokes about sleeping with Ramse's mother. Cole lies down in the travel machine and is told that he is being sent to Philadelphia in 2015. Cole questions if Jones has the right time and location because she was off the last time by weeks but Jones assures him that she has it all handled.
In the past, Cole finds himself next a tank. Cole is suddenly surrounded by soldiers because instead of Philadelphia in 2015, Jones has sent him to North Korea in 2006. Talk about a bad landing spot. Cole is led away by the soldiers and taken to an interrogation room, screaming that he cannot understand the soldiers.
In the 2043 the alarms go off and Jones realises that Cole is in the wrong place. The scientists work hard to track the signal with the intention to sling shot Cole to where he needs to be. In 2006, a General takes a note from Cole's pocket and says that Cole is American, which is good for him. In 2043, Ramse is starting to freak out and Jones reminds Ramse that he is only there because Cole wants him to be. Jones believes that it is Cole's destiny to stop the plague from ever happening. Jones iniaties the sling shot, just as the North Koreans start to beat on Cole.
Cole is then shifted to J.D. Peoples Mental Hospital in 2015. Cole finds himself being escorted into the hospital after assaulting. Dr. Sandman tries to get some basic information from Cole and tells him that he is likely suffering from PTSD. Cole is then told he is going to be hospitalized for 24 hours.
Cassandra is still frantically trying to find information on the army of the 12 monkeys from Jeremy. Cassandra turns to the television, when it is reported that Goines has died of a massive heart attack. This of course is not how Goines died. Frustrated, Cassandra grabs her things and leaves.
At the hospital, as a patient Cole has freedom of movement. Jennifer passes by him to take her medicine and though she approaches him, Cole has yet no idea that Jennifer is the person he is looking for. Cole, a little bit entranced, follows Jennifer until he connects her last name with Leeland. Steps away from the nurses station, Jennifer coughs up her medicine and talks to Cole about her love of primary numbers. Cole asks about the number 12 and Jennifer says that 12 in not a primary and that Cole is not as smart as her. Cole as Jennifer to teach him and she readily agrees, asking him what he wants to learn. Cole asks about the army of the 12 monkeys and what she knows. When Jennifer laughs, Cole pushes her into her room and ironically against the wall on which she drew a monkey. Jennifer says that she cannot talk about the monkeys because it's against doctors orders. When Cole gets insistent, Jennifer explains that there are a dozen agents in her father's kingdom who have eyes like Cole's. Jennifer claims that she set these agents free and got them all shot. Jennifer gets over excited, causing Cole to have to cover her mouth and warn that he will hurt her if he has to. Jennifer then calmly says that the 12 monkeys are her cover band. Jennifer pushes the panic button and when the orderlies burst in, Jennifer tells them that Cole tried to kill her.