Snake is a covert operative under the employ of Sephiroth and goes around sabotaging all of the factions to keep anything from happening to anyone. For any faction to be able to make anything happen, they would have to find and stop him. All of the different factions know that they're being sabotaged, but assume they're being sabotaged by opposing factions.
Disclaimer: This is all entirely fake lore that my friends and I made up.