The Cassie that got pregnant was lost in a parallel time. Cole went and picked up the Cassie from 1957. The pregnancy was thereby erased. So they either don't know that or they are going to impregnate her and that's why she is crying
She had memories of that timeline as well. She was crying because she was remembering more of it and she realized that she is pregnant and that her kid will grow up to be the witness.
Because Time Jesus has special paradox sperm that can cross timelines and Cassie was baptized in a magic red tea bath thus preparing her womb to carry Satan's time-traveling child, I mean, The Witness.
Well apparantly even though the time line was erased, nothing else was she still has the memories of their time together and somehow the pregnancy was not erased either. The messenger guy said to her the witness was created by two travelers outside of time (Cassie+Cole). Can not wait for Cole's reaction when he finds out A. That she is still actually pregnant and B. That the two of them just went and created the destroyer of time that will be one hell of a conversation between the two of them.
Presumably because they splintered so much and have so much of the drug in their system they exist somewhat out of time. The result is when the timeline was altered they became what is frequently called timeline orphans. They still exist even though their timeline doesn't
Cassie is PREGNENT.. they already explained it.. LOVE survives TIME. That baby was concieved through an act of love and therefore continues to EXIST despite the timeline change.
Bear with me here, but if the present Cole and Cassie were orphaned from the original timeline when they stopped the paradox and the actions of the previous "happy couple" timeline did still count, then it still isn't right. Cole would be orphaned from that timeline, but why Cassie? A year had passed in the timeline Cole jumped back from to stop the paradox so even if the splintering and the red tea meant that Cassie was protected from the timeline change it would still take a year for her to "synch" with the other timeline... I think... Jones kept going on about how the real time tethers meant she had to wait a year for them to come back but she remembered the previous timeline so shouldn't the same real time constraint be true for Cassie? What I mean is wouldn't she have to wait for a year for her real time body to "synch" before she would be pregnant? Maybe she will spend a year in the future being indoctrinated and then in 2062 she will suddenly have an immaculate conception.
Either that or she would be a double orphan of two changed timelines, one at the instant Cole stopped the paradox (the new current Cassie, not pregnant), and one when the happy couple timeline split a year from then (pregnant Cassie).
My frickin head hurts... why do I watch time travel shows!
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"If Red Riding Hood shows up with a bazooka and a bad attitude, I expect you to chin the bitch."
Cassie's a brilliant doctor who is also a skilled surgeon. Seems to me that there's little the Monkey Army can do to prevent her from a self-induced or -performed abortion.
To paraphrase the old "Heroes" tagline: Abort the Witness, Save the world!!