27 years after a virus wipes out most of humanity, scientists send a man (James Cole) back to 2015 to stop the plague from ever happening. Cole's only lead is a virologist (Dr. Cassandra Railly), who knows the dangerous source of the outbreak.

Cole returns to the year 2015 to gather knowledge from a patient inside a mental institution. Jones believes that the 12 Monkeys are somehow involved in the pandemic that wiped out the population of Earth, thus making Cole's attempt to extract the information from the patient, imperative. Dr Railly feels that her intervention in Cole's case has given her incentive to continue to help him in his mission, much to Cole's compliance. Written by Peter Iannazzo

We find out that Cole needs to go back to 2014 and find 'the one that got away' named Henri Toussaint who is from Haiti. Meanwhile Dr. Railly working through some issues is helping with the red Cross trying to stop a major plague in Haiti. Cole's job is to find the Henri and find the location of the hidden lab of Leland Goines without running into Railly. Written by Andre Gold

A fight for the future ensues when a dangerous band of marauders hunting for Cole and Ramse threatens the mission to save the past.

In 2011 Jennifer Goines is introduced to the dark room where her father's most secret experiments are taking place. In 2015, she is again in the hands of her kidnappers. Cole and Cassie manage to get into the Night Room facility only to find that that the pallid man has beaten him to it. Cassie learns that Cole killed Henri while in Haiti. In 2048, Ramse learns the lengths to which Dr. Jones went to so as to get the time transporter working properly Written by garykmcd

After the events in the night room, Cole automatically returns to 2043 and finds that the timeline has been altered. He meets Jones, who has no idea who he is. In this timeline, the time transporter is not functioning but a blood tests confirms that they had met previously. A database check also reveals that Cassie was killed in 2015, likely the event that caused the change. He finds that Ramse is in charge of the facility and after some persuasion, he agrees to send Cole back to 2015. To set things right, he has to keep Cassie from being killed. Written by garykmcd

In 2015, Cassie and Cole focus on learning more about Operation Troy. An archaeologist who spent time there reveals that the pottery shard is of Druze origin and that he had previously been questioned by the tall man about the Army of the 12 Monkeys. Aaron makes the connection with former CIA analyst Adam Wexler who is reportedly hiding out in Chechnya. Cole tries to stop a biological attack directed against Wexler and planned to take place in Chechnya. Cole continues to have flashes of disconnected memories. Written by garykmcd

Mr. Cole is the priority, then we worry about the core, Jones tells her team in tonight's episode. She's speaking of the tracer signal: Staying locked on Cole, tracking him in time and space, is the single most important task. All future missions rely upon calling him back, and that need eclipses all others, including the need to preserve the machinery. But it functions as a metaphor for the show as well. Stay locked on Cole and the story stays strong. Lose sight of him and it falters. The characters and emotional arcs of 12 Monkeys have stumbled over its eight episodes, but the story mechanics stayed strong. The show has clearly conveyed the potentially confusing jumps through time and space with seemingly effortless focus, and kept the larger narrative free of distractions by keeping everything centered tightly around James Cole. Until tonight. Yesterday inverts most of the expectations the series has established, not entirely successfully. Cole spends his scant minutes of the ... Written by William Waddy

In 2043, Dr. Jones is in desperate need of a new Core if she is ever to find Cole. The only Core available is at Spearhead but Col. Foster has refused to give her theirs. Faced with few options, she tries one last time convince him to give it to her before she takes it by force. Ramse meanwhile tries to convince his girlfriend Elena to leave Spearhead with their young son. Cole is still in Chechnya but finds himself in 2017 with the virus in the process of destroying most of humankind. He sees Cassie in a TV broadcast and is soon reunited with her in Baltimore. In a scene in 2041, Ramse and Cole come across a group of men and are taken to Dr. Jones. Written by garykmcd

With the replacement core now functioning, Cole returns to 2015 and Cassie and Aaron who thought he had died in the Chechnya blast. He tells them the virus is still out there and Cassie believes Oliver Peters, the man who made the virus, may have kept a sample. Cole finds a connection to 1987 Tokyo and a the White Dragon nightclub. His body is deteriorating however. Prior to Cole's return to 2043, Ramse does what he believes is necessary for him and his family to survive. He and other are now living in a old animal park where he sees something from the past. After an incident, Ramse returns to Jones' lab but finds himself traveling to the past. Written by garykmcd

Cole follows Ramse to 1987 Tokyo and goes directly to the White Dragon nightclub where he sees Leland Goines negotiating the purchase of the 1000 year-old remains that is the source of the virus. Cole can do little to stop the sale however but after a fight where he stabs Cole, Ramse finds himself facing a long prison sentence. In 1988, he begins receiving letters from someone named Olivia telling him he is not alone. Released in 1995, he travels to Virginia where Olivia's identity is revealed. By the year 2011, Ramse has a new role. Written by garykmcd

As Cole is slowly slipping away in 2015, Cassie rushes to find a way to help him combat the ill effects of his splintering before the army of the 12 monkeys finds him. As a result, Cole meets Jones for the first time and has a reunion with his father. Written by Robynne T

Cole has been saved but now can no longer time travel. He is certain however that Ramse will make his way to Raritan National Laboratory where in 2015 the time machine is under construction. Cole's confrontation with his onetime friend leads to a serious injury. In 2043, a new group arrives on the scene intent on taking over the time travel machine. They are successful but everyone is surprised when someone unexpected arrives from the past. Written by garykmcd