Territory points are earned by repelling invasions from other teams. Non-Conquest Invasion missions will degrade the AP of randomly selected enemy territories (displayed as the meter on the right of your territory list, if you own them). When it reaches zero, that territory to revert back to CPU control if the owner does not increase the AP (by defending it) within a certain time period.

Stronghold missions will raise your Territory Rating (both conquest and normal). Your Territory Rating will also increase if the defenses you set up destroy enemies that invade the territory, however this is basically random. Regular Invasions will give you Team Points and damage other teams territories so that they will defend them, although which territory gets damaged is also random.