Back - or ahead, depending on how you look at it - in 2044, Cassie is getting “How to Survive in the Apocalypse 101” training and it’s doing a good job of making her rough around the edges and we like it.
Remember the silver faced gang from the end of season 1 and their stoney eyed- master? Well, they’ve gotten into the facility and we find out that these are the Army of the 12 Monkeys, the babies we saw Olivia watching over in their cribs. The stoney-eyed master guy tells Dr. Jones to send them back into the past. For what purpose? He’s not revealing that - naturally.
Jones refuses and kills off a few of The Army - time travel machine style, ripping them to shreds- but a couple of them escape back into the past to carry out their veiled mission. Deacon (who along with the West have become de facto allies of the facility) shoots and kills the stoney-eyed leader who’s been left behind.
Back in 2016 Ramse and Cole realize that Olivia’s always been one step ahead of them because The Army put a tracking device on him - how quaint. Cole tries to get a doctor (played by Downton Abbey’s Brendan Coyle) to remove it, but the good doctor instead tries to kill Ramse. Dr. Kalman was once in cahoots with The Army but he got away from that life so he feels like Ramse is a bad omen. Cole feels like Dr. Kalman trying to kill his buddy is a bad omen too, so he shoots the good (bad) doctor.
Jennifer! When last we saw her she was about to board a plane that contained vials of the the virus that could wipe out mankind. Jennifer still has the virus but wants someone - anyone - to stop her from releasing it into the wild. Jennifer has a guilty conscious, who knew?
Cole and Ramse track Jennifer to NYC 2016 during Chinese New Year - Year of the Monkey - where she’s about to release the virus. A few dudes from The 12 show up and so does Cassie - with guns ablazing! After Cassie takes out the bad guys she threatens to take out Cole if he doesn’t let her at Jennifer.
Cassie has the idea that if she kills Jennifer she can stop her from releasing the virus. Cole has the idea that that’s just plan mean. They come to an agreement - destroy the virus. They do and …nothing happens…or doesn’t it?
While destroying the virus doesn’t stop the world from ending, it does change when the world will go into chaos and it also effects many of the events that will happen in the future. Back in 2044, Jones rejoices over the team’s small victory and she also gets a new boyfriend who she doesn’t remember, Dr. Eckland (So Say We All, Michael Hogan!), thanks to the switch up in the timeline.
Ramse is thrown into temporal facility jail on because he was willing to risk everyone else’s lives for the sake of his son and yeah, that would piss us off too. The gang later bring Ramse’s son, Sam, to him as a peace offering to get intel on how The Army will strike next. Ramse has no clue and they’re about to kill Ramse when they realize time anomalies - small red pockets formed seeming out of thin air that tear the flesh off of people - start appearing. Ramse proves to be useful when he saves Deacon’s life.
After some digging Jones and the team realize that the members of the 12 Monkeys, known as The Messengers, who were able to highjack Jones’ machine and go back in time went back to 1944 (and other important dates you can track here, with our official timeline) to find special people - think cousins of Jennifer - called Primaries who are related to time. The Messenger’s mission entails killing the Primaries by stabbing them with their own bones and causing time Paradoxes.
The gang sets up shop at The Emerson Hotel, which becomes their base at different points throughout time. In 1944, Cole meets and befriends an FBI agent, Agent Gale who at first thinks Cole is straight out of an H.G. Wells novel - us too!! - but later agrees to help Cole take down the baddies if it’ll mean saving the future.
While tracking down The Messengers in the past, the other looming threats are The Witness and The Pallid Man. The Witness is still an elusive figure with an unknown identity and The Pallid Man is still a creep.
We also learn that The Pallid Man and Olivia are brother and sister types who are vying for the attention of The Witness. The Witness is pissed that Olivia failed at her mission to end the world so The Pallid Man takes over the reigns.
The Witness has a new party trick - he takes on the face of Aaron, Cassie’s ex fiancé, to try and trick her into believing that ending time is a good thing. The Witness also gets inside of Cassie’s head so when she travels back to 2044 she puts the entire facility in danger.
While highjacking Cassie’s mind, The Witness - through Cassie’s body - tampers with the time machine which releases a bunch of radiation into the splinter room, re-splinters some of Jones’ old mutilated test subjects and splinters in bewildered 1950s soldiers who once lived in the Temporal Facility but have no idea where they are no. Basically, chaos.
Amid all the drama Sam gets separated (read: kidnapped) by Cassie who holds him at gunpoint because The Witness made her do it. Cole is able to free Cassie’s mind of The Witness’ hold by making Ramse shoot him, knowing this was snap some sense into Cassie because she shouldn’t let Cole die.
With the machine still haywire, Sam is splintered to a far off time and place. Ramse is stunned and us too because, kids are precious and stuff. Also, Jones’ boyfriend risks his life to save Jones and the rest of the facility by entering the room full of radiation in order to fix the time machine. Now THAT’S love, ya’ll.
Cassie feels really bad - as she should - about ruining everything and Ramse is about to kill her until she reveals to him that while The Witness was in her head she was also in his and she saw a far off place called Titan, which basically looks like the steampunk version of Hell. She believes that if she and Ramse can get to Titan they might be able to get to The Witness and take him out.
Jones has her agenda to send Cassie back in time to 2020 and stop the younger version of herself from ever inventing time travel by having Cassie kill her. It doesn’t work. But what does work is that Cassie and Cole are able to save Jones’ daughter, Hannah who Jones thought was dead from the plague. Turns our Hannah’s sickness was a just meningitis, which Cassie was able to catch in time. Cole and Cassie gave Hannah over to Jennifer to be raised as one of her Daughters.
With limited jumps left and the time anomalies closing in on the facility in 2044, Jones and Cole want to go back to 1957 to find the last Primary and stop the Paradox but Ramse and Cassie want to go back to 1961 to find Dr. Kirchner, the mad scientist they think knows a little something about Titan.
Ultimately, team Cassie / Ramse wins the debate because they enlist the help of Dr. Adler who program the jump - behind Jones’ back - to the year they want go to. Dr. Adler lost his son to the plague so he feels Ramse’s pain. Cole learns that his friends duped him when he gets to 1961 and realizes they drugged him, leaving him at The Emerson Hotel while they head off to Berlin, in search of Kirchner (hey, Matt Frewer!).
Ramse and Cassie find out that Kirchner used Mantis’ (the loveliest Messenger of them all) eggs to create a girl with super human strength who would grow up to become Olivia! Also, while in Dr. Kirchner’s office Ramse spies The Wall of The Witness which includes coordinates for Titan. Kirchner is murdered and so is Agent Gale, Cole’s FBI buddy, while trying to save the team.
When the team gets back to 2044, Cole is pissed at his friends and so is Jones. As the time anomalies start to take down the joint, Jones uses the final jump to send Cole back to 1957 to find the final Primary. He’ll have a year’s time to find the Primary, stop the Paradox from happening and save the future. Cassie, who was originally reeved up to head towards Titan with Ramse, instead follows Cole.
A year sounded like a long time until it wasn’t. Running out of suspects Cole and Cassie find the final Primary too late and the Paradox happens in a very big way. Cassie’s in a coma for nearly a year and Cole goes off and buys a house that looks eearily familiar.
They also make a baby. Awwwww. But then time starts to stop around Cole and he realizes that something’s off. He also keeps seeing this woman named Lillian (Madeleine Stowe, everybody! The original “Cassie” from 12 Monkeys the movie) who reminds us of Jennifer except way more crazy - if that’s possible. She tells Cole to go make some of that red tea, time travel back to the moment before the last Primary created the Paradox and keep it from happening or else the time anomalies of this timeline will inevitability catch up with the world. If Cole goes back in time and stops the last Paradox, it will save the world but it’ll also erase the two years of playing house he and Cassie just shared together. Bummer.
Coles does the right thing - Ramse, we’re looking at you - and he and Cassie are sent back to 2045. They get there in just enough time to head off with Jones to find Titan and save Ramse, Hannah, Deacon, Jennifer and The Daughters from being slaughtered by The Witness’ army. A fight breaks out and then Jones realizes that Titan is a giant splinter machine (created by her crazy ex-husband, ironically) and as its about to blow!
Ramse makes off with one of The Witness’ men who tells Ramse that he can take Ramse to his son. Instead, Ramse ends up face to face with Olivia, who no longer works for The Army, who promises to take him to his son. All this suspense… we hope he gets to see his son in Season 3. Sheesh.
While in 2163, Cassie comes faced to face again with The Pallid Man and a room full of weirdos dressed like less than religious monks. Cassie - full of grit - demands to know where The Witness is. The Pallid Man obliges by touching her belly. Yep, The Witness is inside of her. Created by Cole and Cassie. Surprise, it’s a boy!