I know there's a TV Tropes page for the series. Chapters were initially released on Royal Road but have since been published on Kindle (and I think removed from Royal Road). The main character is an NPC in a VR, female, maybe an elf. I think her first name starts with a Q. She is the "hero's companion", one of three in her village (roughly working out to fighter, mage, and cleric if I recall correctly). They're paired with three "Chosen Ones" of which they know one will be picked by The Prophecy. Suddenly, her best friend starts acting really strange...
While she remains blissfully unaware, we quickly learn that her friend is being piloted by a guy who's great at breaking video games, and is being hired informally to see how he can break the game. There's a variety of behaviors he shows, everything from rolling everywhere to hoarding every miscellaneous object he can get his hands on to solving a combat challenge by removing all of the weapons from an arena before starting the fight. Speaking of which, the two other companions serve as the opponents for the qualifying challenges. After doing all of the side quests, the hero goes to read the prophecy, which he knows will trigger a cutscene that will cut off the village, and kill off the protagonist as a way of heightening the drama of the situation. And so, he finds a glitchy spot in the village which she's pretty sure is out of bounds, and finds a way to cram her into it. As a result, he sees the evil emperor show up, challenge him, and then do some weird hand gestures beside the hero (basically, a cutscene where he kills off the childhood companion). Afterwards he retrieves her. As a result of him doing this, for the most part, the game and its characters do not acknowledge her.
After that, the books basically consist of him exploiting glitches, including the inability of the system to acknowledge her, and picking up new companions, including a bard, a sorcerer, and a ranger. The sorcerer is named "Definitely Not Evil Guy" because he's definitely a spy for the emperor and the ranger is "Sexy Spider Lady" because he glitched her quest and she's a spider monster who acts like she's a sexy elf maiden.
As I recall it correctly, there's a sequence of temples that he has to complete. Each has a choice, but he keeps finding ways to pick both options, resulting in glitches, and that he arranges for the companions to touch the three reward options at the end of each level so that they get all three each time. I remember they also get an animal companion, a tentacled monstrosity instead of the intended otter.
By the end of the first book, the game company has realized that the companion has gained sentience, although it takes them a while to realize that it's contagious (by the end of the second book, it's becoming evident to the reader that the other companions are starting to make plans for how to break free, while the main character remains slavishly devoted to the hero). If I recall correctly, it's eventually revealed that the source of the AI algorithm is a military project, the results of one of the programmers having an uncle in DARPA or something like that. This comes into play around the second book, where they bring him into evaluate the AI, and he starts talking about the possible ways which it could be exploited.
