The protagonist's appearance is only shown once in the entire game. In the original game it was never shown, but in the newly-released Steam Edition, the player is finally able to see what the protagonist looks like.
After killing HER, if you move as she stands there before the screen fades into black, you can see that White Face is, in fact, holding the gun that you used to shoot HER with. He retains his usual appearance, however, the only difference between his appearance here and his normal appearance is that he lacks a mouth, like HER, and he has an arm and a hand.
The protagonist actually bears abilities that one-up those of White Face and HER. The protagonist is able to alter the fabric of the game's universe through changing information in the game's files - something that White Face and HER can't do. Doing a little digging on the protagonist's part can actually reveal a text file written by Ivan Zanotti himself, stating the extent of the protagonist's abilities:
"If you got here it means you're a peeper
White Face can do a lot of things, even create entire worlds: one thing it cannot do, however, is react to you changing stuff with the .ini files.
It cannot stop you from doing that and maybe you'll mess up the game, so please, don't do it!
Wait for White Face to learn how to do that, then try again! Maybe a patch will do...".
Therefore, while White Face is able to create worlds and universes, he can't alter or influence the Protagonist's decisions.
- In the grave level, White Face's arm is awkwardly shifted more ways upward than it would normally be. This is common in most first-person games where the characters can hold guns, where the model's arm is shifted upwards in order for the player to see the gun and arm better.
- White Face missing his mouth could be a reference to how HER lacks a mouth on multiple occasions. It could also be White Face expressing apathy or passivity on the situation.
- Ivan Zanotti has said that you play as White Face in the Grave level because that whole level was White Face deciding it was time to get rid of HER, as she was stealing his spotlight. This could mean you only play as White Face in the Grave level.
- Depending on whether or not you believe White Face and HER to be malevolent, one interpretation is that the Protagonist is actually the true villain of the game. Despite White Face and HER pursuing them throughout the game, their intentions are never to harm the player besides scaring them for their own amusement. White Face even shows throughout that he is affectionate to the Protagonist and doesn't want to die. But the Protagonist is the one who ultimately makes the decision to kill both characters through using their ability to edit the game's files to their advantage, something that White Face and HER can only do to an extent.
- Another interpretation is that the Protagonist is actually the "god" of the game's universe. They have the ability to alter things in the game by doing what White Face and HER can't do, which is to exist externally to change files. White Face only has the ability to communicate externally to the player. So even though White Face appears to have complete control over the game's universe, it is the Protagonist who has more power.