"Think of "Infamous" as a much better version of those open-world "Spider-Man" games Activision came out with a couple years back. Cole goes around Empire City performing both story and side missions in whichever manner he sees fit. If you want to finish all the side missions in a certain area before touching the story you can. If you want to focus solely on the story mode, you can do that to. Doing so, however, will make things harder on you in the long run since you won't have access to certain powers.
By completing missions Cole earns experience. This experience acts as the games currency for purchasing new or improved forms of super powers for Cole. Also, when a side mission is finished, it creates a safe zone in an area of the city where criminals will no longer linger. So in the end, it behooves the player to complete most side missions. "Infamous" does a good job at making the side missions interesting, without having to much repetition. Yea, you will get tired of doing certain types of side missions, like the boring counter-surveillance side missions, but for everyone of those there is an equally interesting, intense..."