So I was toward the end of Mt. Moon when I came across the Team Rocket trio (Jesse, James, and Meowth.) I spoke to Jesse blocking the way, and after I flew through the text, they all just disappeared. Were they supposed to battle me, or was them disappearing like that intended? I noticed another player in the same exact spot in battle for a while, so I figured that I was, indeed, supposed to fight Team Rocket. I relogged to see if they would reappear on the map, but they didn't.

Since I know you where a scripter at DoD i'll go into a bit of detail here.

 

The variable required for many team rocket encounter is named 'KantoStart' if that variable is set to 0 then most team rocket encounters don't work at all as you'd imagine, the only way for the KantoStart variable to be anything other than 0 is to have chosen Pikachu as your Starter, if you did, regardless of you having a different Pikachu at any time of the game, Team Rocket will battle you, multiple times throughout the story, but without KantoStart set to 1, they won't battle you at any time throughout the game as far as I know.

 

This is just a little tease-up from Pokemon Yellow: Special Pikachu Edition, and a tease-up on the Anime.

Ah, I see. That's an interesting way to implement a dynamic NPC/questing system.