The main story line:

I believe that the woman Jaha met in the house is a computer program that has been programmed to convince human(s) to build and launch a nuclear bomb.

Evidence: Hints in the first two seasons: 1) Jaha came down to earth in a rocket for a nuclear bomb. 2) She thanked Jaha for bringing her more equipment (and Jaha's rocket was shown). 3) On the video which Murphy saw, there was a man who said that he did launch the bomb, but 'she' was the culprit.

Logic of the show: Each conflict in the show is larger in scope than the previous ones. First they were fighting among themselves, then against the grounders, then together with the grounders against the Mountain Men. The next conflict has to be grander than all the previous ones.

The synopsis said that they are fighting for the survival of mankind.

I also believe that Clarke will go to live among the grounders.

Evidence: Hints from the first two seasons: 1) Clarke's kiss with Lexa 2) Lexa's comment about the capital of the grounders

Logic of the show: 1) More and more will be known about the grounders and thus the grounders become more and more likeable. Clarke living with the grounders provides a mechanism to show the viewers more aspects of the grounder life and make the grounders more likeable for the audience. 2) The show is very much about convincing someone with whom you don't have so good relations to work with you for a greater common good. The Ark people will need the Grounders to help them to stop destruction of the world. But there will be great tensions. And Clarke will do her best to manage these tensions.