Not that it was in the works, but it could have been a thing. Square Enix could have called it Crisis Core: The Missions.
It wouldn’t be about the main storyline but might include elements from it. Obviously, the plot would have Zack travel from point A to point B destroying enemies to collect items. Just like the game.
The story could serve as a vehicle for Zack to understand what it really means to be a hero. The banter from the supporting cast could shape Zack’s mentality in his quest to become a hero. Just like in the game.
But this is just a daydream of what could’ve been. Still, sounds pretty cool. I’d buy it.