This is Dr. Cassandra Railly, Cassie for short, and she lives in present day 2015 and she works for the CDC (Centers for Disease Control). Cassie enjoys all that 2015 has to offer: free Wi-Fi, to-go cups of coffee and hot showers. Cassie also has a hotshot boyfriend, Aaron, who's a political aid.
Everything's going swell for Cassie and Aaron who are well on their way to yuppiedom until Cassie is kidnapped by Cole who waves a knife at her and tells her that he's from the future, 2043 to be exact. Also, the future's not pretty. According to Cole, a world ending plague is on the brinks of wiping out humanity in present day 2015 and it's up to him and Cassie to stop it all from happening.
More on Cole: He grew up as a Scavenger, Scav for short, in a post plague world with his best friend Ramse (on the right). In order to stay alive, both men have done some unsavory things as Scavs. They also joined and then escaped a dangerous Scav group known as West 7, which is run by a sociopath (we'd bet money on this!) named Deacon.
This is Deacon. He's generally awful and hates Cole because Cole escaped West 7 and so Deacon spends much of the first season either trying to kill Cole or ramshackle the Temporal Facility where Cole and Ramse have found refuge.
This is Dr. Jones. She operates the Temporal Facility in 2043. Dr. Jones chain smokes cigarettes and is obsessed with changing the events of the past so that the plague never happens. She's obsessed with time travel because her young daughter, Hannah, died during the plague, so Jones is trying to change fate. For most of the Season, Cole isn't aware of Jones' ulterior motives.
Also, Jones says "the mission" a lot, and although time travel is really terrible for Cole's body, Cole agrees to do it because saving the world in 2015 means saving himself from living a shitty future in 2043. Cassie agrees to save the future because she's a doctor and that's what good doctors do. The caveat to all this is that Cole splinters - transports back to his time of 2043 - at random points throughout their adventures, which leaves Cassie to wing it on her own.
In an effort to find out if the virus was created BEFORE Leland was shot, Cole tracks down Leland's daughter, Jennifer, who was locked up in a mental institution because she's definitely crazy. With Jennifer's help, Cole and Cassie track down where the virus was produced and destroy some of it but still, the future isn't changed (meaning the virus was STILL released somehow).
Also, as Cole time jumps, he continues to encounter (read: almost be killed by) The Pallid Man, who is merciless and is set on releasing the virus. The Pallid Man is also an accomplice of Olivia, who is equal parts cold and equal parts intent on starting the plague. They both are part of something called "The Army of the 12 Monkeys." The Army serves someone known as The Witness (who we don't really see) who's at the helm of releasing the virus.
Also, during Cole's absence, Ramse finds out that he has a son with his ex-girlfriend Elena, who was also a West 7 Scav and a West 7 escapee. After Ramse meets his son, he decides that the plague needs to happen because if the past is changed then his son won't exist. This brings one of the greatest bromances (Cole + Ramse = Bros for life) in recent television history to a grinding halt. Then, Ramse decides to use the time chamber to go back to the past and use his knowledge of the future, to make sure that the world-ending virus is spread.
Ramse's time jump not only throws a wrench in Cole and Cassie's plans but it also puts him in cahoots with Olivia, The Pallid Man and The Army of the 12; a not so merry band of marauders who are really into making sure this world ending plague happens.
Towards the end of the season, things get a little twisted - as would happen with time travel - so to keep down confusion, we'll only focus on what's important. So here it goes... Cassie's estranged boyfriend, Aaron, basically rats Cole out to Olivia and The Army of the 12 so that he and Cassie can be spared from the virus. Things go left and Aaron is killed in a fire as Cassie doesn't go along with his plan to ditch Cole.
By this time, Cole and Cassie have figured out that the-back-in-time Ramse teamed up with the Army of the 12 Monkeys to guarantee the plague happened (and thus his son was born). They think he's the Witness, but Ramse isn't! Like we said, Dude just wants his son to be born! They confront him at the 2015 time machine prototype, which Ramse has partially helped fund to get himself back to the future and his kid. Cassie shoots him, and then one of the Army of the 12 Monkeys shoots Cassie.
Desperate to save Cassie, Cole straps her into the time chamber machine (the machine's been a work in progress of Jones and her estranged husband since 2015) and she splinters to 2043 so that Jones can help her.
With Cole and Ramse stuck back in 2015, we end the season with Jones and Cassie, gunshot wound and all, in 2043 at the Temporal Facility. Also, they've got company. Specifically, 12 creepy as hell men and women with white face paint - the very same 12 who we see born in 2015 in the care of The Army of the 12 Monkeys. But what do they want with the time facility?