In 2044, the temporal anomalies are getting even worse and one of these time storms is going to wipe out the facility very soon. Cole wants to head to 1957 and stop the paradox that put the hole in time. Cassie and Ramse want to head to 1961 and find the doctor that can lead them to The Witness.
The gang splinters to 1957 and have a friendly drink to get over their earlier argument about what mission to go on. But Cole’s been drugged! By his friends! Cassie and Ramse hijacked the splinter and they’re all in 1961 instead. Cole is NOT going to be happy when he wakes up.
Cole wakes to find that Ramse and Cassie have robbed him and left for Berlin to find Dr. Kirchner. Cole calls on his FBI buddy, Agent Gale from their adventure in 1944, who agrees to help him get in the country but warns him that the doctor is wanted for war crimes by Israeli intelligence and things could get very ugly.
Meanwhile in Berlin, Ramse and Cassie have found Kirchner (and he's played by Max Headroom/Dr. Huxley from Orphan Black)! Unfortunately, so has Israeli intelligence. Cassie/Ramse try to get away but are soon outmaneuvered and kidnapped.
Cole to the rescue! Cole and his FBI buddy find Cassie and Ramse before the Israeli spies can do any permanent damage. It turns out the only reason The Witness and Titan were mentioned in that CIA document is because they came back and said it! They created the clue they found in 2044. This whole mission was for naught. Womp womp.
Or was it? The doctor is wearing the symbol for Titan! Turns out he was responsible for the genetic mutations that created The Messengers. Yep, the Witness traveled back in time, told Kirchner about the plague and had him create enhanced humans that could survive it. Kirchner agrees to take them to his lab in exchange for his freedom. The gang begrudgingly agrees.
Only problem with getting to the lab? It’s on the other side of the in-construction Berlin Wall. No big deal. Everything is going great until Kirchner gets all clumsy and there’s some serious gunplay. Agent Gale decides to stay back and cover everyone as they make a run for it…
Everyone makes it to Dr. Kirchner’s lab where they find “The Sample”, a little girl who was created to be the first Messenger. They also find a map through time which Kirchner calls The Word of The Witness, which we've seen before.
The gang debates destroying The Sample but the 12 Monkeys, lead by The Messenger the gang encountered in 1944, shows up to stop them! There’s a shoot out where Dr. Kirchner is taken out and the Monkeys end up leaving with The Sample.
Having escaped the lab, The Sample is taken to her new home. 12 Monkeys Messenger lady will be her mother now and they will be under the protection of The Witness… not creepy at all. And oh yah, turns out this little girl grows up to be…
The gang makes it back to 2044 as the temporal storm is about to destroy the facility. They have The Word of The Witness (Ramse thieved it in 1961, hoping it would lead to Titan)… but what’s the use if they’re all about to die. Cole orders Cass and Ramse be arrested for their earlier betrayal.