Picking right up where we left off, in 2015, Cole rushes out to save Cassie from the Army of the 12 Monkeys when he splinters and ends up home in the year 2043 – but to an alternate timeline where it appears the time machine hasn't been fired up in a while. In fact, they're using that room as a laundry room now, and the whole place is being run by the VII.
Cole is having a really hard time here, seeing all kinds of weird things and meeting all kinds of weird people including Jones, who in this timeline, is a fix-it person. After a quick test with a microscope, Jones gets on board and realizes that Cole is in a time loop. Worse, Cassie has been shot and murdered in this timeline. AND (it's confusing, we know) it seems her death was the point that changed the timelines and the history.
Cole goes to see whoever is in charge, and it turns out to be Ramse, who has an eyepatch and doesn't believe his story about being from the past at first. When the whole team goes back to the time machine, Ramse tells him how it all went down differently and when Cole tells him that they need to fire up the machine, Whitley freaks out and shoots Jones.
Cole gets into the machine just in time to jump back to 2015, and Jones leaves him with a final warning, one that she instructs him to ask the Jones in HIS time about: that there must be sacrifice. Cole gets in the chair, and disappears into the past.
Back in 2015, Cassie's ex-boyfriend Aaron (assistant to Senator Royce) is dealing with the fallout of an alleged cyber-terrorist named Adam Wexler. That's when Cole pops up and asks a few questions. When Cole finally brings up Operation Troy, Aaron gets on board and decides to help rescue her.
The two travel out to the Night Room as Cassie is led out by the Pallid Man. Aaron misfires a gun and hits Cole while he splinters – and briefly has a memory of being stitched up by Jones. The scar appears on Cole at the present moment, and he also has a clear memory of the license plate of the car that took Cassie. Aaron calls in a favor with his law enforcement buddies.
Meanwhile, the Pallid man speaks with a woman whom we may or may not have met before (and who basically should run a side business doing ASMR tapes because THAT VOICE), and the two come up with a plan to "prepare Dr. Railly." When the Pallid Man protests, the woman tells him that the witness has spoken: and that Cassie is too important – but for what? When Cole figures out that the van had once been used for landscaping, they head to a greenhouse.
And now, Cassie meets the woman we met before, where she's made to drink from a pitcher. The potion has a terrifying effect. Cassie has a hallucination about a red forest with tall grass and finally sees a man there with her: the Witness! In the greenhouse, Cole and Aaron beat up a henchman who gives them Cassie's location.
Cole and Aaron stage a daring rescue operation with guns blazing and rescue Cassie from the clutches of the Pallid man and the Witness and the spooky woman. The plan seems to work: Just as Aaron gets Cassie out of the warehouse, Cole splinters and Aaron, for the first time, sees that this is the real deal. Aaron and Cassie agree to keep searching for the source of the virus, and Aaron thinks he knows where the next clue lies: Operation Troy.
Back in 2043, Cole debriefs Jones and her team. They realize that from now on their focus has to be Operation Troy. Finally, when Cole asks Jones about "the sacrifice" – and Jones tells her that if he succeeds, the sacrifice won't matter, but that he only has a few jumps left before it kills him.