It appears I've caused a sizeable amount of confusion with My Alter Ego #47 (because everything else has made sense until now?). I can see where I went wrong. This is a classic case of trying to fit too much story into too little of a space. Really I should have stretched the concept out to 2 comics instead of just the one, but I want to wrap Skomolii up by #50...so you got the train wreck of #47.
Skomolii has been an interesting experiment in storytelling using the rules of My Alter Ego. Literally I had no idea this whole thing would end with a kid named Saltines, nor did I even know Skomolii was going to kill children. In the case of #47 what happened was I knew what event I wanted to have happen (Dr.Cheese and Saltines meet.) I also knew I wanted to reuse some of the themes that have been recurring throughout the whole story, like a Dr.Cheese location that is labeled as "secret" in downtown St.Louis. It's fun to draw that panel, including new things each time. I also knew I wanted to include the Army's plan for conquest over Skomolii, which involves Saltines. However, what often happens with a My Alter Ego comic is there just isn't the room you think you're going to have. A good example of this is the very short note pinned to Saltines, that note could have said so much more, and possibly not created confusion.
The Army has sent Saltines to Dr.Cheese's secret hideout with the proposal that Saltines stay the night, if he is alive by morning then Dr.Cheese must hand over the antidote for Skomolii, if he dies then he is free to continue farming Skomolii. The Army is assuming that Dr.Cheese will assume Saltines has already eaten Skomolii, therefore if he does not feed Saltines Skomolii then he will explode, throw up his own skeleton, melt, have kittens burst out from his stomach (My Alter Ego #46) and etc. The form of death must be Skomolii.