Before I get on with what I'm theorizing here, just to make sure people who didn't get the memo when they look at the title of this topic, this will have MAJOR spoilers for Version 12.
Now that is settled, the protagonist is one of the most enigmatic characters in the entire game. The few things we know about them is that they are called the Interceptor, they are the only one that can change the future, they had a mother (maybe), they can't die, and they always seem to know more than they let on to certain events like how they know Risa Raider was in the generator room beating up Ren when Aelita went down to see what happened.
Ever since the beginning of the game, you can actually catch a glimpse of Crescent talking to the protagonist's mother about moving to West Gearen to just live a normal life and Crescent also tells Nancy that she only wants to the protagonist smile. This event can be pretty unnoticeable if you aren't looking around.
Than towards the end of the first act of the game, we see that our character dies when they fell into the lava, but than after we seem to appear near a house with a bench overseeing the ocean that Crescent is on. She tells us that there is more for us to do and that we need to wake up and finish what we started.
After some events that happened in the past (with us dying again and this time being saved by Madam X), West Gearen, and the trip to Grand Dream City, when we get to Grand Dream City things starts to get insane. After getting a package with the two people that are from the Unown Dimension and them telling us to go to Nightmare City to meet the Puppetmaster. The Puppetmaster starts to tell us something in a riddle and after that they tell us that we are something called the Interceptor.
After the course of going through the Future that we made by saving Vivian instead of her sacrificing herself, we died again after the alternative future version of Melia uses decimate with her Yveltal and we protected Melia by blocking the blow. Madam X notices what we are and Melia was just left to only thing about this event.
When we return to Grand Dream City to investigate what Team Xen really is and what the Miera region is, Melia starts to look for what the Interceptor is and she found out what the protagonist is.
And during the course of being in the past again, this time in Hiyoshi City, we found a vacation house that is right near the Rejuvenation Co. which is now the Xen headquarters in the present. When there the protagonist starts to have repressed memories and a single figure that looks like a ghost telling us that they were going to be with them forever or something.
The same thing happened again when we were in Zone Zero, but we saw two people that could actually be the protagonist depending on the character that we choose and another memory in the Pyramid with a character that was named Adrest and another character that he called mother. After that the protagonist than begins to talk with the font color being green instead of the normal white.
After all of this, I still have no idea what the protagonist is. They seem to be from the past, but how exactly did they manage to get to the present is beyond me. And now he game is starting to focus on the protagonist more since version 9.
Where this is going, is mostly up to the Devs of this game since they are the only ones who know what is going to happen in the story beyond version 12.