Because The Great Reason isn’t alive. Why exactly do you think Stephen goes around as it’s Agent, leading Flynn?
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Because that makes no sense. Stephen has no reason to.
It wouldn’t even be Shin Megami Tensei at that point
what are you arguing anymore?
Okay? He showed up, and did… nothing, and left. Stephen is a neutral force, he could’ve stopped YHVH at any moment, he simply protagonist out of sheer entertainment.
Your justification for “it’s an out of universe reason” are very fundamentally flawed, because the logic you present breaks immersion and is, bluntly, very foolish. Why did the Saiyan Saya happen if the Angels can see across universes?
Why didn’t Hagaromo give Minato Six Paths chakra and prevent Minato from dying against the Nine Tails?
You are arguing from not only possibility, but just genuine ignorance in the basis of story-telling and engagement. You’re planning to be a writer, so I can’t see how this concept eludes you.
Why give any protagonist challenge, when Stephen could just give them a Persona, in-which he can’t. Why not bring in another unrelated character from a foreign universe to make it easier on the protagonist?
What purpose does Stephen have, dragging an unsuspecting character from any random point in the story, telling them “fight YHVH”, do for the plot?