In 2043, Dr. Adler inspects the new Core and everything seems to be working perfectly; Cole is in 2015.
Suddenly he hears a noise and discovers Ramse has turned the conference room upside down looking for the splinter injections. He knocks Dr. Adler out, places him outside the room and sets the teams research on fire.
Back in 2015, Cassie and Aaron are planning a vacation and rekindling their romance when Cole walks through the door. “You can’t be here” Aaron shouts. Everyone realizes it’s not over. Somehow the Army of the 12 Monkeys got their hands on the virus. Cassie remembers Oliver Peters’ involvement and it’s decided he needs to be located fast.
Cole and Cassie arrive at Peters’ lab and discover his husband has been killed by the Pallid man; Peters is gone. “We destroyed the virus but not the man who made it” Cassie says. That’s why nothing’s changed.
Cassie discovers a journal containing Peters’ notes for creating the virus. In it, they see an image of the Annapurna Remains (aka the Origin of the virus) excavated in the 1980’s. They also spot a photo and Cole remembers his conversation with Wexler about Tokyo and the White Dragon. He assumes Leland Goines and the Army of the 12 Monkeys are connected somehow.
Cole splinters back to 2043, while Cassie goes in search of Dr. Peters.
When he arrives at the temporal facility, Cole tells Jones everything starts on November 21, 1987, in Tokyo at the White Dragon. However, she shares the bad news that Ramse torched all their research.
Elsewhere, Ramse enters an amusement park where other survivors (including) Elena are living. He tells her he wrecked the lab and made off with the splinter injections. She realizes Jones' men will be coming for the injections, but he promises they will be long gone by then.
The nomads known as the Daughters are spotted near the amusement park and Ramse sees the familiar monkey symbol. He approaches their camp and mentions the Army of the 12 Monkeys. Jennifer Goines steps out of the caravan.
Meanwhile, at Project Splinter, Cole’s condition has worsened. Jones has him placed inside a reconditioning system for molecular stabilization. It won’t reverse the damage, but will keep him alive a bit longer. She asks if Cole knows where Ramse might be, which he does. Jones gives her word Ramse will not be hurt, and Cole provides the amusement park details.
Jennifer tells Ramse the two of them have work to finish; to undo what they’ve done. She talks mostly in riddles, mentions the Witness and hands him the familiar pendant belonging to the Pallid man. Jennifer tells Ramse he’ll need it later.
While this meeting is taking place, Whitley and his men enter the amusement park and Elena is accidentally killed. Whitley shoots and kills the man responsible for her death.
Jennifer sends Ramse on his way. He returns to find Sam kneeling beside his dead mother and promises he will always protect him.
Surprisingly, Whitley tells Jones he will not go after Ramse. With whatever time they have left, he should be a father to the boy he tells her.
In 2015, Cassie asks for Aaron’s help and the two locate the latest shipment of macaque monkeys while searching for Dr. Peters. Those rare monkeys were the easiest way to track him down. Inside a large shipping container, Cassie finds Dr. Peters who tells her he completed the virus. The Army of the 12 Monkeys threatened to kill his husband unless he recreated the virus. He soon realizes Jason is dead, and begs Cassie to kill him. After all, he could recreate the virus easily from memory. She tells him to disappear, and spares his life.
Meanwhile, at the shipping yard, the Striking woman tells Aaron that Dr. Railly is very important. She asks what he's willing to do to keep her alive.
It doesn’t take long for Ramse to appear at the temporal facility with the splinter injections. He simply would like a word with Jones and wants to be left alone. Ramse catches Whitley off guard and manages to escape; he makes his way to the time machine.
As the facility's alarms begin to go off, Jones asks the team to revive Cole and set the time machine for 1987.
Ramsey confronts Jones, and places a bomb on the time machine. Max enters and distracts him but shots ring out. Jones makes off with the bomb and disables it. Max is killed during the shootout and Ramse finds himself locked inside the time machine room. He injects himself and forces the sole scientist in the room to send him back. “I promised my son I’d always protect him. I can’t do it now, I’ll do it then” Ramse says.
As Ramse prepares to splinter, Cole appears at the window and watches his friend vanish though time. Since Ramse was never synchronized, they have no tracer signal to bring him back. This was a one way ticket for him.
Jones sends Cole to 1987 warning him this is the endgame, he has no jumps left. “You must find the source of the plague and you must eliminate it” Jones says.
Ramsey survived the jump, he's now in 1987 and will do his best to stop Cole.