Conspiracy theory time
What if Alfred was the head of Court of Owls all this time and that's how he knew everything and he kept batman under his radar as he was a vigilante to make sure court of owls could be kept a secret. And when Bruce found out the truth he knew that the court of owls functioned from the very ancient arkham asylum and Wayne mansion because he sheltered the leader all this time, he blows everything up and erases everything, killing himself in the process.
But he doesn't say anything to any of his children in his last message in fear that Alfred will kill his children too.
Nobody doubted Alfred because he raised Batman and since Alfred basically had access to anything and everything thanks to Bruce Wayne's and Batmans reach and talented hacker "grandchildren", he could make sure nobody actually realized that "Court of Owls" wasn't just an urban legend but an actual organization with Alfred as head. Alfred later turns Batman and Little Damien Robin into Talons after their death. He wanted to turn Jason too but he was taken from grave before that.
Since Alfred was supposedly dead and wasn't supposed to survive the explosion of Bat cave he was in a dilemma since he couldn't have access to any of batmans kids and all the kids had their own head quarters.
I think the read plot twist will be if in the Game Gotham Knights, Alfred is revealed to be the head of "court of owls" all this time.