The season finale concluded night three as the third and final episode.
Series co-creator Terry Matalas confirmed a few points in interviews and Twitter comments in the aftermath of the Season 3 finale marathon:
Athan Cole never was the Witness - the one shown in earlier seasons, communicating to followers via the House of Cedar and Pine and red tea leaves, possessing Cassie, etc. Athan could have been the Witness but after his redemption chose not to be. But there wasn't an alternate timeline in which he was the Witness, which then changed to it being Olivia - it was always Olivia, and Athan mistook his visions of the Witness to be his future self.
Mallick staged the attack on Olivia's camp that mortally wounded Ramse's son Sam, in collusion with Olivia. They were both in on it - all a Machiavellian plan to motivate Ramse to want to kill the Witness - which in turn would motivate James Cole into doing what she wanted. Olivia took Sam and raised him for years with the express purpose of killing him later to fulfill her goals. Everything that transpired was according to her plan - except that Athan would both survive and choose to reject his role as the Witness, then come back to save everyone. Olivia thought she would kill Athan-the-Witness to take his place, but in truth she always was the Witness.
Jennifer Goines has been prominently repeating the mantra "Climb the stairs, ring the bell" based on her time visions. Matalas pointed out that she has been saying this since Season 1 ("Shonin"), and it means something.
Matalas posted a photo of James Cole's birth certificate: he was born in Pennsylvania, his father's full name is Matthew Cole, and his mother's full name is Marion Woods.