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It's 2015, and at the CIA headquarters in Langley, a presentation is underway describing Project Troy. Now, what the CIA is after here, is to take down that leaker of classified information: Adam Wexler. They can't do it with an airstrike, so they'll do it with a disease, which, by the way, is the likeliest form of the deadly virus that wipes out humanity.
Meanwhile, you know who's having a hard time since the Army of the 12 Monkeys drugged her? Cassie Railly. Cole's here to help her and the two of them aren't collectively doing so well. They decide to head off to find Dr. Edward Garret at the museum. Also, Cole is pretty in love with Dr. Railly, gang, and he proves it to her – after eating all the Tandoori skewers – by dancing with her.
Dr. Garrett tells Cassie that the artifact Cole has taken photos of points to a religious sect called "The Druze" AND it originates in the Ukraine. Bing! She asks him if he's heard of the Army of 12 Monkeys and he freaks out and tries to escape. That's when Cole decides to rough him up, and learns that the Army has already approached Garret, and they've roughed him up. When Team Virus-Search (Cassie, Cole and newly Aaron!) figures out that they CIA is about to kill Wexler with the virus, they try to formulate a plan, but Cole splinters back to the future, telling them that in one week, they have to give them all of their information on the Operation.
Back at Senator Royce's office, Aaron lifts the key fob out of the Senator's pocket, and hacks into the computer to find proof that the CIA is behind all of this. But there's a twist! Cole calls Cassie from the Ukraine and tells her that Operation Troy is happening RIGHT. NOW.
See, two hours prior, Cole was in Chechnya looking into things when he saw the case containing the virus. He asked a cab driver to follow the car the guy with the briefcase was in, and rides along on a great chase through the mountains. Just as Cole catches up to the bad guy with the case, a sniper takes out the bad guy and then starts shooting at Cole as well.
Turns out, the Army of the 12 Monkeys is trying to intercept Operation Troy. But Cole has intercepted them so he calls Cassie and says she has to tell him (in the future) exactly how to destroy the virus. Got it? Basically, Cole is calling to tell them to make sure that in a week's time, they give him all the right information he needs. They agree to help, as always, but Cole is taken hostage by the Army and driven to a fortress where he comes face to face with Adam Wexler. Not believing that Cole is the right man, Wexler opens the suitcase and the virus is released! All this while Cassie and Aaron try to convince the CIA that Operation Troy has been compromised.
As Aaron and Cassie deal with Senator Royce, who is SUPER angry about this key fob getting stolen, Cole is getting the stuffing beat out of him by Wexler's henchmen. Cassie tells Agent Pratt what she knows about the virus, and he admits that the Operation is not going well. In Chechnya, the soldiers are getting sicker and sicker as time goes on, and Cole begs Wexler not to let anyone leave the compound. But the soldiers have a plan – to give Wexler up to the Russians in exchange for health care. And that would be devastating.
After Wexler decides to take matters into his own hands and shoot some of his own people, Cole reaches Cassie via cellphone and tells her to burn the place to the ground before the Russian military arrives. Even though it means the end of Cole too. Turns out that Wexler knows about the Army of the 12 Monkeys as well. Wexler tells Cole about an incident in Japan in 1987 at a place called the "White Dragon."
As Cole waits for the airstrike that will kill him and burn the virus from all around him, he tells Cassie that she mustn't, in the future, tell him that he's going to die. They share a moment about the process they've been through so far, and Cole tells her that he was too embarrassed to tell her at the time but the answer is the "Florida Keys", as in the place he always wanted to visit as a child. And the airstrike happens.
So now it's a week later and Cole has just arrived at Cassie's place to get all the information about Operation Troy. Cassie takes a moment to really try to get to know him, feeds him cheeseburgers, and then…sends him to his death.
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