>>713059510To certain extent, yes.
While 95% of Main Story missions have you using pre-determined team, there is one point where you have to use your own units.
Since in Blue Archive character max level is tied to your account level, and your account level goes up when you spend your AP, if you have not been doing that then that part of the main story is literally impossible.
...Good news is spending AP is incredibly easy. If you don't care about clearing the missions, you can just sweep any stage that you've three-starred (easy as shit on earlier ones) and just dump everything into those.