12 Monkeys The Series FYI

This is true, it just wasn’t the one everyone was expecting.

Because he wasn’t the Witness, he never was.

She didn’t know either way, it’s not like she told them who the Witness was supposed to be at any point, they had to figure it all out on their own. Primary doesn’t mean all knowing.

The Witness did dream up all the end of the world scenarios and did everything else the Witness was supposed to do, it just wasn’t the person everyone thought it would be. They DIDN’T know who they were serving, even Olivia didn’t know she was serving her future self and even makes a comment about it when she realizes she is the Witness and not Ethan. And yeah, it is supposed to be strange and convoluted, that is the nature of time travel.