Red Queen

is the true Boss in this game, and she was the GOD, also mother of your creator. Same as your creator, she was in blood form. Although she only appear as true Boss during last quest Guinea Pig, but you will have already heard about her if you listen very carefully with chat to citizens and check documents.

She was the reason for not only this epidemic but also for other big disaster happened in the past. Defeat her will not kill her but put her back into sleep.

Boss
This was the only boss that do not have fixed level, it's level will based on how many citizens you have embraced. So the more citizens you embraced, the higher level for her. If you haven't embrace anyone, she will be at level 30, and if you try to embrace all others she will level up to 51 (I did not embrace the pillar citizen, so maybe even higher if these 4 pillar citizen also embraced).