Keep playing the liberation missions on your map. There are 3 general "districts" in both cities that you must complete. Check your Liberation Missions map above your normal map to see each divided district. See your logbook if you want to know what kind of missions need to be done. Your best bet is to do all of the viewpoints (the bird icon). The missions only appear if you have been near them or have the viewpoint unlocked. After completing them, you then have to talk to your "contact" to complete one main mission usually involving assassinating someone.