Even though this is a porn game i really enjoyed the story, and a part in the science fiction class made me think about this theory for the good ending: I basically believe that alpha MalO is incredibly powerfull and smart, and it may even be Capone, and every time that we lost our memory our own MalO didn't lose it because she is non corporeal and she just lied about also losing it, why?, because she and the other MalO's were attending meetings with eachothers to try to "expand" but they realised that the cages that the scientist woman was putting into them was stopping them from doing that, so they formed a plan, -and this is where i get to the important part of my theory-, Alpha was going to make everyone forget by making a very powerfull electro charge, and then they would fill their hosts with false memories to get rid of the cages and also be closer to them, that's why our MalO was acting when we woke up like if we were married, because she wants us to believe that. So to summarise, Alpha MalO earased everyone memories with his powers so the other Malo's may be free from their cages and gasligth their owners into being more together.
I may even write a fanfic about all of this.