A conflict that occurs at around the same time as the one you're dealing with. The secondary one may be completely unrelated to you, your goals, or such, but it significantly affects how you can go about doing your thing.
The first video game about Secondary conflict was released on November 1992.
You are not a soldier, or even fancy yourself a warrior, so you're working as or for something else during a war even when fighting breaks out near or around you.
Note that "secondary" only refers to it being something NOT tied to the conflict your're personally trying to solve, and so something you don't want to involve yourself with at all, but it still brings difficulties to dealing with your own problems.
Best cases are where the player does NOT solve the secondary conflict to deal with their own.