As the title suggests, this will be detailing how to make a gamer story work in the world of naruto, it will explain how to scale stats, how to use abilities, possible sources of the power and eventually how characters/clan members would interact with it. This obviously are suggestions only, feel free to do your own thing.
Let's starts with the origin of such power.
Where could an overpowered ability capable of fucking over reality in more ways than a hardcore tentacle porn fan could imagine?
The first, and most used is B.O.B (bastard omnipotent being), or some call him/her R.O.B. (Random omnipotent being).
This is the laziest and less creative possibility but can be done well. I would not suggest using it for a fanfic with a serious theme, as it makes the reader understand that the protagonist is pretty much a chosen one and will not die, or only will at the end of the fic.
You can get around the lack of tension due to plot armor by making B.O.B. into what is essentially Nyarlatoteph, and for anybody who lacks knowledge of Lovecraft's work, is a near omnipotent being who fuck around with people for amusement and many tend to prematurely die, you can also give a spin on this by making the ability one inheritable through killing its last owner, but don't abuse this, as it will make it hard to connect to a character when you believe they can genuinely die any moment.
If you plan to make a less serious fic then B.O.B. is a good way of doing this. Breaking the 4th wall and saying the author gave the power is practically the same as this
The second very used (and abused) way is leaving it unexplained.
This can be annoying to many, but overall doesn't change much for many readers. Again, for less serious fics it's perfect.
You can also get around this by vaguely suggesting that something from the first option happened, but not showing and explaining it
A third possibility is a kekkai genkai mutation or something similar to that (yin-yang release, special senjutsu etc.)
This is… hard to make believable, while the sharingan is a very bullshit ability, it has many drawbacks and doesn't give nearly as many possibilities for OP outcomes as "the gamer" does. The hardest thing to explain is how? Why would a genetic mutation create a video game? I personally feel that it's better to leave it unexplained instead of this, it allows the reader to explain it to themselves instead
A forth possibility is the canon one, Gaia/Gaea, the embodiment of earth, giving this gift to the user.
In the canon webcomic source, it's a mystery why earth would give such powers to anybody. In the narutoverse, it could be simply assumed that it's to stop the Otsutsuki from absorbing all of its energy.
The idea makes sense as in Boruto we are shown that the shinju tree does kill the planets it absorbs the energies from. And even ignoring that the main naruto verse confirms it uses nature energy, and even corrupts it.
Would earth have enough energy to make the gamer work? To those who might ask this question, I would remind you that all of Kaguyas chakra was gotten from the nature energy of the earth.
The fifth possibility is the canon deus ex machina, the sage of six paths.
Is there much to explain? He wants world peace, wants for Kaguya to be beaten, gave Sasuke and Naruto moon busting powers can bend reality, and he could be used as an excuse for a SIs soul to be thrown into the Naruto world too!