Shortly after the watch incident, Cole tells her to meet him in two years at the John Adams hotel, and then Cassie watches as Cole disappears before her very eyes. Time travel. It's a real thing, team.
And now a little flashback. Well, flash-forward. See, in the future 2043, Jones the time travel scientist tells Cole that he's going to go back and change the world. He gets on board, but it also doesn't feel like he has much choice.
When Cole tells Cassie that his game plan is to shoot Goines on sight, Cassie is upset and tells him he can't just murder someone. Cole tells her not to worry, he'll disappear instantly and it will erase the future.
The team does some major work-ups on Cole and they discover that his body is not like other humans. He has overactive adrenal glands, his brain works like he's constantly having a grand-mahl seizure, it's a lot.
After Cole shoots Goines and kills him, the terrifying truth is revealed. That killing Goines didn't stop the epidemic and it didn't change the future. So someone ELSE must have been responsible for releasing the virus.
It wasn’t Goines at all. It turns out that the world was ended by something called the Army of the 12 Monkeys. All along, they’ve been looking for the wrong person. Or people. Or even monkeys possibly.
But there's a link! This is Jennifer Goines, the daughter of the now-dead Goines. She's drawing a monkey on the wall, she's just been made a very rich woman, and she's totally insane. Ladies and gents, the ride has just begun.