Season 3 starts with Cassie on the good spaceship Titan. Pregnant and wanting to go home, an angry woman named Magdalena informs Cassie that she's just a vessel, but won't necessarily be who the baby thinks of as a "mother." Don't worry, Cole thinks he may have found where she is and he's not far away.
Cole will stop at nothing to find Cassie. Because he knows that she's carrying their unborn child. What he doesn't know - is WHO that child is. Yes, it's true. Cassie and Cole are the parents of The Witness.
Also, there are splinter SUITS now. How it works is - the Army of the 12 Monkeys can jump back instantly to warn themselves about what's to come, thereby solving their problems before they even begin. And then they sacrifice themselves so there's no paradox. Can you imagine?
The Army of the 12 Monkeys spends a lot of time trying to protect this box of precious cargo. Which turns out to be SUPER precious and holds The Witness as a baby. Magdalena and friends all go through time, raising him and educating him.
Ramse, meanwhile, is found by Olivia, who convinces him that she knows how to stop The Witness once and for all. Angry and full of dread because his son (RIP Adult Sam!) has just died, Ramse agrees to team up with her and brings her to Jones' compound.
Jones is suspicious of this whole enterprise, and locks Olivia behind an electric fence. Olivia tries to strike a deal: Jones gives her the machine and she'll give them The Witness. Jones ends up torturing her. And it turns out that Ramse and Olivia have hatched a plot to kill The Witness at the source...
Ultimately, after a lot of difficult dude-feelings between Cole and Ramse, there's a chase and Cole shoots Ramse to prevent him from killing Cassie. It's devastating and sad that these two brothers made it this far, only to part ways like this.
The whole team swings through the 1980s to steal "The Word of the Witness" map out of an auction and Cassie and Cole finally have to deal with the fact that they are the parents of The Witness. A secret that Jennifer Goines keeps from Jones.
Now that they have the big map of The Witness' visions, Cassie and Cole journey to the 50s where the Army of 12 Monkeys is recruiting people by preying on people in states of grief. They realize that their chance of stopping The Witness - lies with killing him as a child.
Jones prepares the team to travel back with the splinter suit and an Electromagnetic Pulse Device that'll disable all electric current around them. So the team will have a window where none of the bad guys can escape by using their splinter vests. Also, turns out you can sync the suits and they also can set you on fire.
But Deacon and Jones are starting to get suspicious when Cole didn't save Ramse, and Cassie seems to be acting funny. Seems like they're holding a few secrets. She looks into it and begins to unravel who everyone is. Finally, she discovers that Cassie and Cole are the parents of The Witness.
Jones goes to visit Olivia, who tells her that Cassie and Cole are learning to think like The Witness. Jones believes that Olivia can help, and so she lets her go, much to the anger of Jennifer Goines, who is still trying to keep the whole work family together.
Deacon, Hannah, and Jones chase Cassie and Cole through time. They catch up to them in oldy-timey London, where they find out their son, The Witness, (whose real name is Aethan) - is a good person. Who maybe can be saved.
So, then there's the story of The Witness. Traveling through time, and learning all he can about it, he ends up falling in love with a woman named Eliza. Real, impressive, amazing kind of love these two.
Eliza dies. First she is murdered and Aethan is able to go back in time and save her with his splinter suit. But then she dies of natural causes. Aethan goes back in and tries to save her 607 times. But every time, she dies. Of a deep vein thrombosis.
Learning from a trip back to visit Cassie Railly that time is really the enemy when it comes to saving people, The Witness prepares to go back to Titan. And carry out his destiny of stopping time forever. But Cassie and Cole turn up for one last time to try and stop their son from, ya know, killing the world.
Through some major trickery and time jumping, the family Cole ends up at the house of cedar and pine. The origin of The Witness. In a very tightly timed series of events, their location is ascertained by…
Olivia and her red tea. She travels back to the time stream to find them. When she tells Jones the news, the team leaves immediately and locks her back up. But as they all arrive at the house of cedar and pine…
All of Titan arrives in 1959 at the house of cedar and pine! What follows is a crazy firefight standoff. Knowing that this is their only window to kill The Witness before he gets back on Titan, Jones and Hannah rush inside…
And then, a major twist. It turns out that all of this time, Aethan was not The Witness - Olivia was! This is news to her, but it all falls into place when she realizes she's now doomed to go back and lead the Army of the 12 Monkeys, and trick HERSELF into all of those steps. The proof comes when she murders Aethan.