If we see somebody, we are either visiting them or meeting them (generally for all good reasons).
A doctor advising his patient to see him after a week of taking medicines. A secretary telling her client to see him on Tuesday for the deal... and so on.
But, here is my context.
Harry did too bad to me by making fun out of me. Unfortunately, in front of everyone, I could not do anything but warn him for the consequences --"I'll see you" and then I left the place.
Here, I will see Harry but this seeing is different! How should I use see somebody that does not mean meeting/visiting for all good intention? Taking revenge or teaching Harry a lesson does not require me meeting him personally! So, here, actually, I don't see him.
When a hero says to a villain that he'll see him, does it merely mean meeting as in the general context? I don't think so. The hero uses see metaphorically and does not meet the villain. He may simply damage villain's properties making him riches to rags! And the hero goes off! Where did he see him? :)
In Hindi and my mother tongue Gujarati, see you literally means I'll screw you when the time will come.