SPOILER WARNING! This page is only meant to be read after you have seen all of the character endings in Virtue's Last Reward. I also recommend playing Nine Hours, Nine Persons, Nine Doors before you read this. Be sure to solve all of the puzzle rooms in hard mode to unlock all of the endings, and make sure to check the flow chart thoroughly to ensure that you haven't missed anything.
Who is ? from the true true ending?
There is an ending that you can unlock by solving all of the puzzle rooms in hard mode. It will appear below the Phi ending in the flowchart.
If you choose this ending, Kyle's body will wake up in the infirmary, although it soon becomes clear that whoever is occupying Kyle's body isn't Kyle himself. Nobody specifically says who it is, and it's just referred to as "?".
In a Twitter post, Kotaro Uchikoshi (creator of the Zero Escape series) seems to say that ? is the player.
Considering the fact that ? knows all the details about the Nonary Game that just took place (as Phi points out), the only other possibility is that ? is a powerful esper who has managed to see everything that just happened in the game.
Who is Brother?
Brother's identity is unknown, although since Alice says that he was a very old man at the time when they were planning to attack the Free the Soul headquarters in 2028, the only known character who matches that description is Dashiell Gordain. It has been said that Gordain had died and had successors by the time Hongou was forced to play the Nonary Game, but this could prove to be false. Gordain was alive in 1912 (he survived the Titanic disaster), so he would have to be in his 120s or 130s. There is at least one confirmed real life case of someone who lived to be that old (Jeanne Calment), so it's not entirely impossible.
There have been theories that Brother is Light or Santa from 999. However, Brother is said to have had a divine revelation and created Free the Soul when he was 26. The first Nonary Game took place long before Light or Santa turned 26, and that Nonary Game was effectively run by Free the Soul (Hongou was in charge, and he was doing it for Cradle Pharmaceutical, which was under Free the Soul's control by then). This means that it is unlikely that either of them is Brother, unless their consciousnesses switched places. It's possible, for example, that when Light was knocked out and placed in a coffin, his consciousness switched places with Brother in the past during that time.