We open at a CIA presentation, Oliver Peters (Leland Goines' Rolling Stone), is discussing Project Troy. A deadly virus he created and weaponized.
The CIA has had enough of whistleblower Adam Wexler and plan to take him down using Peters' virus. A virus that would kill every one in that very room in a couple of hours.
Elsewhere, Cole and Cassie follow their only solid lead - the photo of a plate with a monkey - to Dr. Edward Garrett. Cassie confronts Garret at a benefit event and he informs her the artifact belongs to a religious group known as "The Druze." Where are these guys based? That's right; Chechnya.
Later on while making plans with Cassie and Aaron, Cole begins to splinter. He asks them to gather solid evidence on Operation TROY, to give him when he returns in a week.
Aaron quickly takes action swiping the Senator's jump drive and finding proof of the CIA is behind this madness. However, Cassie gets a surprise call from Cole warning her that Operation TROY is happening at that very moment! Confused yet?
He explains to her exactly what to tell his future self in order to destroy the virus once and for all.
Our time traveling hero arrived in Chechnya a few hours earlier and tracked down the briefcase with the virus. When a member of the Army of the 12 Monkeys kills the CIA agent with the case, Cole grabs it and runs off with the briefcase.
It doesn't take long before Cole is captured and brought to Adam Wexler; the whistleblower. Ignoring Cole about the contents of the briefcase, Wexler opens it releasing the deadly virus.
While this is taking place, Cassie and Aaron try to convince the CIA that Operation TROY has been compromised. Realizing they've lost contact with their agent Chechnya, they opt to work with Cassie to resolve the matter.
Back in Chechnya, all the soldiers in the compound are getting sicker by the minute. Cole pleads with Wexler to do the right thing and die there, rather that spread the plague.
Wexler eventually comes to his senses and kills his own men, getting wounded in the process. Cole then contacts Cassie via satphone warning her the virus was released and to burn the compound immediately.
Before he dies, Wexler tells Cole he knew about the Army of the 12 Monkeys specifically an incident that took place in Tokyo in 1987 at the "White Dragon."
With the airstrike approaching, Cole warns Cassie not to tell his future self that he's going to die there. Obviously that would create another alternate reality. The two discuss their time together and he confesses that the Florida Keys is the place he's always wanted to visit. Then the place goes BOOM!
A week later, as expected, Cole arrives at Cassie's place for the information he ask for on Operation TROY. Though Cassie struggles with her choice, she ultimately respects his wishes and keeps his fate to herself.