1: They're just Gangs such as the yakuza, cartel or just random gangs and scavengers.
2: Spaceship or Portal probably. (The game is still being developed and i'll think of something along the way)
3. He can go back in time. (It'll effect the whole multiverse)
4: How this Entity is destroying universes is using gamma ray that is extracted from stars.
P.S: I didn't plan further with the story. It still a prototype and still developing but I don't expect this to go far