itch.io

That good to hear. I hope that even a fraction of the ideas are put into place, but just make sure that you don't make it so wide with random content that it becomes shallow. I have seen to many good ideas be ruined by that. This seems to be your first game, so keep it tight, that way you have a strong foundation and goals. If the game is not huge but deep people will want to play more.  I like to use VoTVs map as an example, it is not that complicated but the simplicity allows them to make everything feel impactful and permit, compared to a massive open world map (New Far-cry games) that can feel quite empty.

Now this is were I would be cautious. I  think that the story mode might not be a good idea, you would be making two different game-play and focus types. Stick with one and make it right.  People will buy an add-on/dlc for a good game more often then get a bloated mediocre one.  I have made that mistake myself and the projects never got off alpha stage :(.

From what you have presented, keep it as is, and integrate the story elements with the MAL0 ally game-play . You don't even rely need to change what you have made already, instead make an upgrade (reach the current max GBs LV) that comes in one her emails to you to help next game play update . She can kind of be a tutorial, being not that aggressive and helping the player to understand the hostile AI without it being OVERKILL.  

For the reward system here is an idea. You might just have to remix it, perhaps you make the getting  scene become the challenge?  A tug of war of ideas, she can have some kind of extra want or dislike certain items ect. Peev her off and she will try and take control, a hidden way for the player to find more scenes(always fun :3). It adds a bit of flavor, the player needing to push her to dom-mode and can allow a reason to lose that is not game over, but hidden options for people who like it and people who don't. Just remember what is your core game-play what we are talking about could be considered late stage additions depending on what you want it to become.

Speaking of witch, what do you want the game to be?  I can see a few paths from what you presented in this alpha, but are you trying to do all or is one the main focus above all else?  I will say that if you continue with the lethal company game-play it could be fun with more players (One plays MAL0?)  but that is a lot of work. If it is the story I feel you will have to make it apart of the map tiles (exploration will be king in understanding what happen here and why she is with you ect.) And I will warn though we all came for the FUN stuff if that becomes the totality you really will be setting the bar high as your competition as is more than just games at that point. 

What ever it is I hope you stay true to the why you wanted to start doing it in the first place. This is something that has sparked my interest and I would love to see it reach 1.0
 

let the player talk to malo and start any previously viewed scene, maybe bedroom variants.
unlock more scenes and story progression through gaining intel.
possibly block the player from increasing level until challenges/story elements are met.

add more ways to deal with malo, like throwing things at her

story progression could involve finding other dungeons full of other hot SCPs