The MC accidentally gets a powerup that changes him so that he isn't TECHNICALLY human anymore. Then a god/admin/will-of-the-universe that hasn't been explained yet teleports all "humans" off the earth when monsters start to spawn.

Since the MC isn't technically human, he gets the fun of struggling to survive on his own on a monster-infested Earth...

1. The main character gets powers and monsters show up in a modern setting.
2. The world itself is made into a fantasy style setting. Everyone else is put into a safe zone, and the main character wanders for 50 years. He doesn't get to see other develop their own "normal human" power system to deal with the setting, and instead he uses his own weird system
3. The main character arrives at the post post apocalyptic city with existing factions vying for power within the city.
4. The main chatacter immediately leaves the city before encountering ANY hostile political faction, and goes to other cities that we are told are worse than our starting city.
   
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Such as skipping the powers in modern world parts, skip straight from intro to fantasy world (where he goes through a power testing phase), and have him encounter minor cities for several years before he encounters the major one filled with political intrigue.