We fully expect the week of San Diego Comic-Con to be a time for big news about major franchises, but nobody was quite expecting this. It's being reported that Disney has severed all ties with James Gunn following the recent resurfacing of a collection of tweets he wrote several years ago in which he made jokes regarding some very unfunny topics. While this obviously means that James Gunn will no longer be directing Guardians of the Galaxy Vol. 3, this decision could ultimately change the franchise, and by association, the entire Marvel Cinematic Universe, in some pretty major ways.
What we know about the current state of Guardians of the Galaxy Vol. 3 is that James Gunn had already submitted the first draft of the script to Marvel. Therefore, the first question becomes, what happens to this script? Does Disney's decision to cut ties with Gunn mean that they won't use the script that's already been completed? It's possible they could start the film from scratch in order to be sure no trace of Gunn is associated with the movie. Of course, there's some question about whether or not the film has enough time to do that. Guardians Vol. 3 was expected to drop in 2020, likely in early May. That gives a new screenwriter less than a year to write a new movie in order to begin filming in time to make that date.
Even if Disney does decide to keep Gunn's script as it is, it's highly unlikely that Marvel will be 100% happy with the first draft. No writer gets everything right the first time. That means rewrites, and those rewrites will absolutely be handled by somebody else. These changes could be minor, but if, for example, Marvel takes issue with the way the current script ends, any rewrite would significantly change where things go from here and almost certainly in a way different than how James Gunn would handle it.
Even if the plot doesn't change, the flavor certainly well, if only because any other writer will have different taste in 70s pop music.
From there, the movie needs a new director. A cast that has now made four movies together will have to work with somebody totally new. While Gunn may not have directed the new Avengers films, he was still very much involved in making the Guardians work in those movies. Will this new person fit in well with the existing cast and crew? Will the actors be as comfortable with this new director or will they have trouble working and taking direction from somebody new? Even if Marvel finds a replacement who is skilled, it's possible any replacement will have trouble picking up this franchise. Any new director will also have a different vision of the material.
James Gunn had previously stated that Guardians of the Galaxy Vol. 3 would be the end of the road for the current iteration of the Guardians, but we have no idea what that means. Was Gunn planning on having some characters die or leave the team? Rewrites could end up changing where any character actually finds themselves at the end of the movie, which will, in turn, change where they can go in the future.
While Spider-Man: Far From Home is currently set to be the official beginning of Phase 4 of the Marvel Cinematic Universe, we know that a lot will change after Avengers 4. Marvel has made no secret about the fact that the MCU will take on a more cosmic focus, and that Guardians of the Galaxy Vol. 3 was going to play a huge part in that. If the movie changes drastically without James Gunn at the helm, how will those changes in turn change where Phase 4 goes from here?
Of course, there is one other, fairly drastic, but worth asking, question. Will there even be a Guardians of the Galaxy Vol. 3? It may seem crazy, and it's certainly unlikely, but one way Marvel could deal with this the issues it now has to consider is to scrap the entire idea. Depending on how the Guardians are left at the end of Avengers 4 the film might not be strictly necessary from a storytelling standpoint. Avengers: Infinity War brought the characters to very different places and one expects the next Avengers film will take them even further. Maybe that place will be a good enough ending for this team and Marvel just decides to move on.
We'll never really know how things will change from here because we'll now never see what would have been. Guardians of the Galaxy Vol. 3 will almost certainly happen, but what it will look like is anybody's guess.