I"m trying to get those trophies for taking over territory in all the districts but I'm confused to how it works. I finished the game with evil karma so all the good side missions are locked (I did all evil ones) but are those needed for full take over?
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No, you don't need to do both evil/good missions. There is a good karma mission for every evil so no matter which way you play you can takeover all areas. Just finish all the side missions. Some side missions are triggered by getting into a fight with enemies, after you take down an enemie a side-mission icon appears. I think it's the same for both games (Infamous and Infamous 2).
Completing all side missions, including the secretive ones gets tricky. Just keep your eyes peeled for any enemies circling around in the areas of the map that aren't already covered in white. When you look at the map, notice how there's a white outline around the island. For the island to be taken over, all the spaces need to be filled in.
When you've stumbled across those last few enemies in the empty spots, putting them all down will result in one of them glowing should you be so lucky to come across this specific set of baddies. Either turning up a secret package to find or a convoy mission to disrupt, the completion of all tasks will finally serve you the trophy on a platter.