Berlin 2016. Ramse is being chased through the streets. He's blocked on a bridge. Olivia steps out of a car and tells him his time is up as it was preordained by the Witness.
What they don't know is Cole is around and this is a trap.
But they didn't anticipate they would be outnumbered.
They escape unscathed and go underground. They start to understand that every time Ramse is on top, they managed to find him.
In 2043, Katerina is forced by the 12 to send some of them back.
Katerina has saved Cassandra but Deacon is not on their side and whatever Cassandra tries to tell him to change his mind, he doesn't bulge.
Cole tries to stop Cassie from Killing Jennifer who has one of the vials of the Virus in her hands.
Cassie explains how they found out when the plague started and how they can stop it.
Cole insists he can persuade Jennifer not to do it. Jennifer, as insane as she is, always had a thing for Cole and gives him the vial.
They then proceed to get the rest of the vials and destroy everything. They know they've changed something, they all felt it but Cole still protects Jennifer and it forces Cassie to strand him in 2016 while sending Ramse back to 2044.
2044, Cole has a picture of him and Cassie from 1944. They know they've been there but Cassie seems very reluctant to go.
Ramse is still behind bars and he begs to see his son again.
Katerina must try to accept this new universe but can't seem to be irritated by Dr Eckland whom she was with before they changed the timeline.
Without knowing where the 6 messengers were sent, they only have one choice : go back.
The time variations seem very unstable which allows them to send them even further back. However, Katerina explains they might not arrived at the same time.
Cole is sent first then Cassie. She ends at the hotel where Cole meets her.
Jones ends up turning to Ramse for help in an effort to get Cole and Cassie back from 1944.
But as soon as he gets there, he's hit by a car and can't stop the events. Thompson is killed as before.
The Messenger has disappeared and Cole and Cassie are detained.
As they understand what the 12 Monkeys are trying to do, the 2044 Jennifer Goines reveals they have to find her in 2016 and she insists that it has to be Cassie and not Cole that goes.
In 2016, Jennifer Goines comes regularly at the Hotel hoping Cole comes back. She seems stable, taking medication and has some friends.
In 2044, Ramse and Cole know that Deacon will always be a problem because of all the enemies he made over the years and they decide to take care of it.
1975. Cole and Ramse travel to New York City to try and stop the Twelve from another Primary.
In 2016, Cassie Helps Jennifer with her medication but she is still reeling from her experience in the red forest.
Cole faces the Witness as Cassie's hallucinations continue. Some deadly visitors from the past show up as the time machine malfunctions and starts to tear apart time and space.
After the recent losses, Katerina finally realizes that she needs to be stopped. She asks Cassie to go back in time because the two of them are responsible for all they have lost. Cassie has one mission : kill Katerina before she conceives the idea of the time machine.
By the time Cole learns of their intentions, it is too late, Cassie has been sent back.
He is sent back at exactly the same time but unbeknownst to him, they are now in a time loop. Cassie assures him she has already killed Katerina and tries to prove it to him.
2016. Jennifer Goines forms The Hyenas to take on the 12 Monkeys' organization and with Cole's help, they discover a plan to acquire the virus.
2044. Ramse asks Cole to ask Jennifer about Titan. While Cole lies about what Jennifer tells him, Hannah, Katerina's daughter, tells Ramse and Cassie where they might find information from the past.
Cole, Ramse and Railly are at odds at to where to go in the past. Cole focusing on the last primary wants to go back to 1957 while Cassie and Ramse want to go to 1961 and get the doctor mentioned in the CIA documents they obtained.
Cole and Katerina decide to go back to 57 and Cassie and Ramse can't do anything about it, or can they ?
The temporal facility is a step closer to destruction and Cole goes to 1957 to save humanity while everybody else looks for Titan, the stronghold of The Witness.
Cole and Railly try to stop the final paradox whilst Ramse, Jennifer and Deacon find it hard to survive the apocalypse in an effort to find the Witness.