At this point, all is not lost

It's still early in the season, and there are many PL games to play. United has 29 more PL games to improve things. Yes, there are still issues with the club's structure. A director of football is still needed.
However, these are points beyond Mourinho's scope, and he can only control what happens on the pitch and how his own players perform and are coached.
The Chelsea game shows United, when they want to, can enhance things and match the best. And Chelsea whilst not many's title favourites definitely have been amongst the strongest starters.
If Mourinho can steady the ship, and get a respectable league position and better results, then he may well ride out his "third season" malaise.
Can all be rosy again, soon? Who knows? But it's a chance to reset the mistakes.