Amazing episode.
After a hard thought of this....what if Cassie was the witness the whole time posing as the the 12 Monkey leader.
1)Throughout the season, the witness always wore the plague mask, something Cassie mentioned in the beginning of the season as she was obsessed with the bubonic plague in attempt to deceive the woman, Ramses, and the creepy man with the scar.
-Cassie realizes in the future what the initial plans were with the lady and scarface so she "replaces" the leader and goes back in time. This makes sense that in order for herself/Cassie to go to the future, she needed to tell Cole where the machine was in the last episode.
2) When Cassie was kidnapped, she never sees the witness' face for the same reason Cole couldn't see himself from a different time.
3)The red forest/plants that was explained to Cassie from the witness could have been only been known by Cassie because she was the only person to see the plants. Maybe it was a hint for that particular part?
4)This whole thing had already happened already. The witness/Cassie lied to the lady that Cole would disappear (so they won't hunt him anymore) and that Ramse would die (she thought he died? when she went through the machine ).
