At the end of the game, the character has a choice; stay or leave.

I've picked both, and it doesn't seem to matter.

What does seem to matter is whether or not your follow the other pods instructions when there's noise in the data stream. That seems to be the difference between ending D and ending E.

So, does it really matter what answer you pick for that question? What changes?

Given the options for 9S' ending, there could have been four outcomes, but since staying on earth or leaving with the machine's ark doesn't seem to matter, I'm not sure what the point is.