According to Mission: Impossible - The Final Reckoning director Christopher McQuarrie, the framework for Top Gun 3's story "is already in the bag."
When asked to elaborate, McQuarrie replied, "It wasn't hard. I thought it would be, and that's a good place to go from is you walk into the room going, 'Come on, what are we going to do?' and Ehren Kruger pitched something and I went, 'Mhm actually,' and we had one conversation about it and the framework is there. So, no, it's not hard to crack. The truth of the matter is, none of these are hard to crack. It's as you start to execute it, and as you start to interrogate it, as you start [to think] why these movies are made the way they are. It's not the action, it's not even the level of or intensity of or the scope and scale of the action [or] the engineering around the action, it's none of those things -- it's the emotion."
So it sounds like McQuarrie will be involved with the writing process of Top Gun 3 along with Ehren Kruger, as it was initially reported a year and a half ago. As far as whether or not he's going to direct the film, McQuarrie replied, "I have given that absolutely no thought whatsoever. I have done a lot of research into how to make a Tony Scott movie." Many people have been trying to make Tony Scott movies, and most of them have been failing horribly, so those are big shoes to fill, even for a seasoned director like McQ, as everyone calls him.
Our lives are the sum of our choices. Tom Cruise is Ethan Hunt in Mission: Impossible - The Final Reckoning.