Idea 1:

The game takes place after the first one. It is similar to the first. Emily is now a tyrant who abuses her citizens with new designed technology. You are a soldier of her army who refused an immoral order (a massacre for example), you are arrested and escape. While you were doing prison time, the Outsider visits you. You become the Robin Hood or Stalin, by protecting the people from terror or by killing everyone including Emily . You would cause a coup de'etat, bringing to power a new government. The new government could be a republic or a Communist society depending on how you play.

Idea 2:

You are a British soldier (or somewhere which resembles Britain if it takes place in a fictional universe) in a war which resembles WW1. After a massacre during an over-the-top mission, you are deemed a coward after suffering from shellshock. You are put into a dark room, where the Outsider visits you and grants you power. You escape and decide: will you kill everyone or try to end the war using a non-lethal method?