"Fact": D&D is about party cooperation, and it sucks when the DM makes one PC - or worse, an NPC - the Chosen One Who Is Destined To Save The World while everyone else are just sidekicks.
"Fact": This is how, like, every other goddamn fantasy novel is structured.
Note: This method will work best in tabletop, face-to-face D&D.
Consequently, I propose the following way to handle this in D&D. It's a decent plot idea, even if it's overdone to death. I mean, like, if it were a steak, it would be ash. But it's so hard to do in D&D it could easily be done a little more often, at least without sucking.
So the PCs, typically four of them, are the party of sidekicks. There is no PC chosen one, and no NPC chosen one. There is just a fifth PC, controlled by literally every player. This is not a new concept, unless by "new" you mean "since the indie gaming explosion" - several indie games do multiple authorship.
The Chosen One (or whatever your campaign term for it) is created by committee, leveled up by committee, and taken care of by the players' solo characters. The DM can set special rules, give the chosen one lower stats, or more, or whatever. The Chosen One's actions are also decided by the players. A means of deciding who can speak in the voice of the Chosen One should be determined - raising your hand, or passing a stick or something. It shouldn't be too much of a problem; players will get used to it. More active players will talk as the CO more often, just like they talk more anyway.
In combat and stuff, the players also control the CO. This should be fairly simple, actually, since D&D combat is tactical, and often there really is a "best" choice. The CO could also be a bumbling swineherd, thus giving the players the chance to make the CO screw up intentionally, to give their solo-authored characters a chance for heroics. Again, in the heavy structure of D&D combat, this will be pretty simple. Normally you toss some dice, then sit around silently for ten minutes, or play game boy or something. But with the CO, everyone gets to participate in combat twice a round.