Very fun idea, that will need some balance changes for it to work out great. I love the randomness. In the end after about 20-25 runs i made it to the 10k health boss and died there. My observations are:
There are a few pieces to your militia that get your far automatically. There is A LOT of pieces that just wont work at all, i was skipping so many additions to my deck, because they would not synergize or just hurt me.
I think a kind of weighting system and a slight priority weight for essential key synergy pieces is needed.
E.g. i get a thousand ferrets but DARRRRRR is never showing up (doesn't matter if i take a ferret early or wait to see if he shows).
Few times the first boss rolled me, because i just couldn't get anything. Well, that's rogue for ya i guess. But just adding blindly until the third boss and realize there is zero synergy but i could not improve it by my choice is frustrating. That happened a lot in those runs. When i got a synergy rolling, suddenly nothing would appear that makes sense (like having a bunch of hellhounds on the board but nothing to remove unnecessary additions and/or nothing to improve my situation beyond the "One part" hellgate addition.) Sure, my sample is small. But it feel like it could have some work done to enable runs. Not to make them easy and always work. But to nudge it a little to the synergies.
Another problem was beating the first bosses to fast as it limited the additions i got. No reward for a victory sucked too.
Bosses stack health a LOT quicker, than there is any gained defenses or my offense can deal. The pacifist seemed weird to me and the only other real one is a medkit that shows up rarely.
Androids didn't give each other the +1 for the one time I managed to recruit 3. (bug maybe)
Else, loved the art. Was laughing about the hell hound corgis. Beauty of an idea. Keep on working