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In 2043, Jones is smoking and talking with grouchy old Dr. Adler, and hang on to your hats, team - because this one's a doozy. So, back we go to 2015, where Jones is a researcher in Manhattan, chatting with her father in a bar. She's not going back to Berlin, as her father requests, because she is hard at work on the top secret Project Splinter. Off she goes to Astoria, where Cassie Railly is waiting for her, in the bushes, with a gun.
Cole, meanwhile, is starting to have some seriously bad dreams as he recovers in Cassie's bookstore apartment. We've seen it before, the shattering glass of milk, the blood on the ground, and Cole is really going through it when Aaron wakes him up. Cole has a seizure, and Aaron saves him with an injection, and that's when Cassie finally convinces Jones to return with her to the bookstore.
Back in 2015, when Cassie and Jones discuss the idea of a paradox and that sparks Jones's imagination: if they can get blood samples from the original Cole, who is now a child – they might be able to save his life. All of this proves too much for Aaron Marker, who goes to see Olivia and tells her he wants to make a deal to save his life and Cassie's life in exchange for information.
Things get super weird at the gas station where Cole's father works when Cassie and Jones find younger Cole and ask his father for permission to take some blood. Cole, Sr. pulls a shotgun on them and tells them to skedaddle when Cassie mentions the Army of the 12 Monkeys, and that piques his interest. It turns out Cole Sr. has heard that before – from Cole's mother. (Wait, what?!)
Cassie takes blood from younger James Cole, and as she does, older Cole gets up to see what's happening, which nearly causes a paradox. So instead, Cole learns about his mother, who hid Cole with his father because she was on the run and couldn't protect him. And that's when things go way off the rails. Cole Senior goes outside for some air just as Aaron comes to take Cassie away.
The bookstore is raided by Olivia's henchmen and the Pallid man. And that, ladies and gentlemen, is where the shattering milk and the drop of blood flashback come from. Cassie grabs younger Cole and escapes just as the Pallid Man catches up to all of them and kills Cole Senior. Finally, as the Pallid Man comes into the bookstore, Cole creates a paradox by injecting himself with his own younger-version blood and explodes. Yes. He explodes.
But it turns out that the paradox process actually has healed Cole. He can't travel through time anymore and younger Jones agrees to try to forget any of this ever happened and goes off into the future alone (also, we learn she's pregnant...and we all know what happens there. But at least she temporarily gives up smoking). Meanwhile, younger Cole is put in foster care meets a new friend for the first time: yep, Jose Ramse.
Finally, back in 2043, things get pretty hectic when some really spooky looking people with oddly colored dead-people faces attack the compound. (Woah! Who are these people!?) They want into the compound, and they've gotten a familiar face to help them get in: Deacon – the leader of the West VII.