Silver storm Studios is a small team, and we were recently wondering how to write a story-based video game? We have a lot of ideas and a plan for the story has been set in place. However, it seems we are struggling to decide how we are actually supposed to write a story that can be turned into an actual game. So, we were simply wondering if anyone had any tips for us or can tell us what direction we need to head in? If it helps our game style, we are trying to develop is based on the Bunny graveyard. At least in terms of the style that takes 2-d art and the story combined with minigames. I'm sure there is a name for this genre but that is the best descriptor I could think of write now!

They're called point and click / Hidden-Object Puzzle Adventure / Roll Playing.

Sites with a lot of these types of games are: Bigfishgames.com and Toomkygames.com.  I'd recommend you download and play a few to get an idea of what to do. (Bigfish you can play a demo free for 1 hour which is probably sufficient to give you a good idea ). Toomkygames gives you the full game for free. 

how we are actually supposed to write a story that can be turned into an actual game. 

You can turn any story into a video game, the issue you'd need to deal with is how the gameplay would be. There are many answers to that. My suggestion is to play or at least watch story heavy video games and see how their story is delivered.

At least in terms of the style that takes 2-d art and the story combined with minigames.

I haven't tried nor seen Bunny Graveyard yet but I suggest that you not to stick with minigames. 

Your question is pretty vague. Usually the story is already designed to fit a specific gameplay style (e.g. something like Ace Attorney clearly won’t fit an FPS game), so forget the plot; it sounds like you guys can’t work to design a game in the first place.

That is if I understood the issue.