Cole was missing for most of the episode because he needed to recuperate for what might be his last jump, which I highly doubt. Cassie and Aaron were working on finding the doctor who created the virus. Here's a great idea, tell Cole to go back in time and kill this doctor, so then the doctor never ends up making the virus. It's just a thought. Anyway, Cassie finds the doctor, but decides not to kill him because what's the point when he already made the virus. Aaron, on the other hand, ran into Red Forrest Woman and seems to have made a deal with her in order to keep Cassie from dying because Cassie is very important. Obviously, it doesn't work if she isn't in the future, but again, whatever.
This show deals with a question that was at the heart of Fringe: how far would you go in order to save someone you love? It seems like Cole and Aaron are asking themselves the same question.
Out of all the people who survive in the world, I can't believe Jennifer Goines is one of them. I can't believe a group of women actually took her seriously. In 2043, she meets Ramse and tells him Cole can't stop the plague. Ramse asks her how did it start to which she answers only The Witness knows. She hands him a necklace for later use. Ramse goes back to his camp only to find his son motherless. He goes on a rampage and in the end, kills Max, who I'm not going to lie, I totally forgot about her ever since she left the West 7. He sends himself back in time to 1987, which makes him a very likely suspect to be The Witness. Cole was planning to go there anyway (to stop the plague, what else?) but now if he runs into Ramse, he'll kill him.
So Goines also mentions that death changes things. It can be both cause and effect. As we witnessed before, Cassie being taken, which would have most likely led to her death, changed the future. She would have died before her time. Since Goines said Cole can't stop the plague and Ramse is now in the past, who does Ramse have to kill to stop the plague from happening?
I have this theory guys that is kind of out there. What if next year they restart everything with a new Cole? That's right, I'm talking about a Groundhog Day scenario. The first episode of the 2nd season would be Cole meeting Cassie for the first time and throughout the season we could see what different choices everyone makes. It would be pretty cool.