Sollux hacked a regular game of Pokémon Red and Blue.
A simple sprite edit/replace is definitely something he would do in his spare time, and being him, he'd take it all the way and leave exactly two original NPCs remaining, replacing the rest with people he knows and characters from video games. He then decided to challenge himself and completely break the game while still leaving it functional, hence Kanto's geography being seriously out of whack, the sidequests making very little sense but being unskippable, and the absolute lack of logic.Terezi, Ganon, and John were swiftly replaced as Gym Leaders, and we will eventually meet their replacements.
When the party was told to meet at the Seafoam Islands, it was specifically stated that all the Gym Leaders were there. However, Terezi, leader of Pewter Gym, was not already there (Eridan had to tell her to come, just like the rest of the party), Ganon exploded, and John's in the hospital (however, John has shown signs of being able to teleport, having been left behind in Celadon yet appearing to rescue Dave in Cinnabar). Therefore, there must be three new gym leaders taking their place. Aside from this, the author seems to take any excuse to shoehorn in new characters, so we should meet their replacements soon, as well as Adrian Brody's and Link's, since they died later on. The story is written entirely in-character as Dave.
Because really, you know he'd publish something like this. Professor Oak is working with the villains
Oak somehow knew about Team Bad's plan to kill Dave even before Dave left his lab, so at some point he must have communicated with them, as Team Bad would have had no reason to publicly announce it or anything. Also later on in the murder mystery chapter, Oak is seen having a casual conversation with the evil Elite Four Boss while he was cooking dinner for Dave's party. There's also the fact that Oak invited Elite Four Boss and Team Bad to a party meant for Dave in the first place. Either Oak is beyond stupid, or he's plotting behind the scenes to kill off Dave. Thor was working for Professor Oak
According to The Other Wiki, Thor is the god of (among other things), Oak Trees and the protection of mankind. Therefore, he's good friends with Professor Oak, and wanted to help him protect Dave by giving him HM 01. This is just an attempt to make a worse fanfic than My Immortal.
Well, how else would this exist?