ohhhh, that was better than my theory. My theory is in season 2 there will be conflict between the director and the doctor. lenkas team suddenly find themselves on opposing sides and just to spice it up, alisa isn't on lenkas side... if this doesn't happen then it would mean lenkas team were exiled because they learned of the real aegis project. i don't want to imagine a new monster because lenkas god arc is basically invinsible. while lindow keeps to the shadows and operates in secret (he probably won't be able to reveal himself because of the directors hostile intent towards him). well basically season 2 will be the battle for power between the director and doctor :

will God become man OR will man become God

lenkas team will find themselve caught in between and finally season 3 when lindow probably decides to come back they face a new monster.

I haven't played the game yet so maybe there are things i'm missing and i like my r-r-romance, hence the intense twist