Does it make a difference which faction missions I choose in Just Cause 2?

The sphere of influence of a faction grows when I complete their missions. Are the areas that those spheres can extend to mutually exclusive, or do my actions decide which area has which occupant? Does my support for individual factions make a difference later in the game (e.g., by not being able to complete missions for another faction later)?

The areas of faction influence are pre-determined, your actions in different areas won't make a difference as to where the factions take control over.

There is also no scenario you can enter that will make any of the missions unplayable; you will be able to achieve 100% completion regardless of how you approach faction missions from the start.

This is what the complete map will look like.

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