Main character is a game fanatic. One day he finds a game that he thinks will be interesting, he downloads it, the game's concept is to use a scan feature to scan what you look like, then use that as your character, its a simple game but it looks like there are a few bugs. He finds a mod made by the games creator, he installs it but what he didnt expect was to actually meet face to face with the creator, who is this creator? Kami-sama! Kami sama arrives by teleportation through the console. Kami sama explains that the game is actually a game that kami sama plays often, but to humans, its know as their lives, yes, this game is basically a control of earth.
The next bit I dunno about, there are 2 scenarios I could take
Shonen (battle) : he installs other mods to his own body and tries to free humans from this game
Non battle (mental battles): uses the game to get rid of anything that makes the world bad in the world, if he makes the world a better place, kami sama will release them from the game