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In Tokyo in 1987, Ramse arrives post-Splinter, steals a coat, and stumbles around just as Cole arrives. They're both headed to the same place: The White Dragon, the bar where Leland Goines remembered meeting Cole. (Sidebar: The music is great there!) Leland is meeting with some businessmen about buying the remains of a 1000-year-old dead body. What Goines needs is a "stellar sample" from the past. When Cole and Ramse make themselves known, Goines' henchmen make them fight each other. In the process, Ramse stabs Cole and escapes, but Goines DEFINITELY wants that old corpse now.
So then Ramse goes through many (many) years in Fuchu Prison in Japan. Because he doesn't have a social security number, the 80's American Embassy guy can't help him. So, he spends 1988-1990 getting beat up by an angry guy in the prison yard. In 1990, he gets a copy of The Art of War from a pen pal named Olivia, who knows he's a time traveler and wants to help him. Finally, in 1992, he gets even with that bully (using the principles from the books!) by revealing to the rest of the prisoners that the bully is actually a jailhouse snitch. When Ramse is released from prison, he comes face to face with Olivia, and we've seen her before: she's that "you are walking in a red forest" lady!
Olivia takes Ramse and the Pallid Man (and some senior citizen hangers-on) out to the swimming pool in the backyard, puts everyone's amulets in a tray in the center, and then creates an explosion that turn all the plants red.
You know what's interesting about Ramse? He doesn't seem to age, which could be some time travel thing or he just has good genes. Also, since he has a memory of the past, he knows a lot about how the virus comes around AND history a general. Which means he can make a lot of money on the stock market, which helps Olivia have lots of money to go to Markridge/Leland Goines and invest in manufacturing the virus (Crazy right? Ramse is helping invest in the virus that made his life miserable, but inadvertently created his son). Some things make more sense now, and by 2014, Ramse realizes that Cole has started showing up in this timeline and there will be more visits to come. This is about the time when Leland Goines goes to visit Jennifer in the hospital and finds her still obviously nuts, demanding she keep secrets about the lethal virus in the Night Room (which, of course, we know all about from Episode #5).
We then learn that all the present day (i.e. 2015) action that has happened since Episode #1 has been done with Ramse completely aware –and ordering Olivia and the Pallid Man to let events play out as they should (or in some cases, ORDERING the events to play out as they should). But, now that Oliver Peters has created the virus and with Cole presumed dead (because Ramse stabbed him in 1987, his last jump) - the only thing left to do is to fire up the plague itself.
So, back in 2015, Aaron returns to the bookstore after the announcement that Senator Royce is running for President. There's more to that story, though – turns out Aaron has been let go from the campaign because he's a political liability, but he'll land on his feet. When he asks the Senator about the "private sector project" to create protocols for widespread disease outbreak, Royce considers it. And best of all, the investor on that project has showed up – it's Olivia.
Meanwhile, Jennifer Goines has been found hiding behind a dumpster, and is taken back to the Goines house, where she takes a bath and gets her hair brushed by Olivia, who casts a spooky sort of spell over her (also, should Olivia run a professional ASMR business? You decide). Outside the room, Ramse talks with the Pallid Man about his future. And back in 2043, Jones takes a risk when she realizes that Cole could be dying, and "Slingshots" him to 2015. Ultimately, though, the risk is unsuccessful and Whitley tells her the worst: that they've lost the tether. Cole is lost.
With everyone abandoning the project and running off to other places, Jones tells them she will not be leaving, that she'll breathe her last breath in that splinter room. As she puts it: "Hope is the luxury of those who are unburdened by fate."
Wait...so what's Ramse's ultimate plan after releasing the virus (which, as mentioned, will ensure his son is born). And is he the Witness, the seeming leader of the Army of the 12 Monkeys? Also, does Olivia have a second career as a voiceover artist? Because she should.