Undertale Theory on the nature of the protagonist (Spoilers)

This post is for people who have actually played this game to completion.

Don't read it if you intend to play it and haven't yet

I have been wracking my brain trying to piece together the Chara/Frisk/player connection and this is my working explanation. Feel free to tell me whether I'm on the right track here.

Most people seem to think that you are playing as Frisk and that Chara aka the first fallen child that you name at the beginning is a separate character. The obvious reasoning is the ending of the pacifist run where Asriel essentially told him that he isn't Chara and that Frisk behaved nothing like Chara. Also in the genocide run Chara became a separate entity that ended up attacking the player.

However, the curve ball is at the end of the pacifist run when you then reload Undertale. Flowey had a heart felt plead begging the player not to reset the world and erase all the achievements (and character development from Flowey/Asriel). he directed this message right at Chara not at Frisk.

Trying to fit this all together in a way that makes sense. I'm concluding that the player you are controlling a synthesis of Frisk soul and Chara's determination and this essay is my rationale.

My view is that after Chara died. His body was brought by Toriel back to ruins and buried in the bed of golden flowers. Chara was essentially a soulless being similar to Flowey his soul merged with Asriel and is presumably destroyed after Asriel died. However similar to the way Asriel lived on due to determination in the body of a flower, Chara inhabit the body of Frisk. However they differ in the source of determination as Asriel remnants was injected with determination but Chara's determination was inherent to his personality. 

If you notice the caskets at the basement of Asgore castle, Chara's soul was red as shown in the casket which was the same colour as Frisk throughout the game

If you notice in the snow-golf game. Each colour of the human soul represents different aspects of humanity and presumably the characters of the previous human

Bravery = Orange. Justice = Yellow. Integrity = Blue. Kindness = Green. Perseverance = Purple. Patience = Light Blue.

As it was established that determination was the source of the power to "save/reload" and Flowey specifically plead to Chara not to used that power. Also the primary used of the save/reload function is to escape death and whenever we die we hear Chara's memory. I'm going to infer that the colour Red represents "Determination" and this determination is from Chara and not Frisk. Frisk who had his own soul but adopted Chara determination (and hence turned his soul red to match Chara) when he fell and landed on the burial site of Chara.

Whenever Frisk died you end up getting flashbacks from Chara memories of Asgore telling him to stay determined that gave Frisk the power to go back in time. Or when Frisk had the temptation to live with Toriel at the ruins and not escape, message came to stay determine from Asgore about how Chara is the future hope between monsters and humans which prevented the player from just giving up the adventure and you get flashbacks from Chara's life with Asriel during the final boss encounter that helped Frisk "save" Asriel. To me it was Chara determination that drove the adventure of Undertale

So what was Chara's determined about? 

Well we know that Chara deliberately consumed buttercup to poison itself so that Chara can merge souls with Asriel to escape the barriers to get 6 more human souls. Depending on your playthrough this can be interpret two ways

1. Chara was a troubled and evil person who hated humanity who poisoned Asgore and laugh about it and left the underground to kill the humans and obtain their souls and become powerful and godlike.
2. Chara was a troubled but ultimately well-meaning person who was willing to sacrifice its own life to allow Asriel to escape the barrier and to bring back six human souls to liberate the monster kingdom. When attacked by humans, Chara wanted to kill them in self-defence. The poisoning of Asgore was a prank gone wrong rather than a deliberate attempt and the laughter was more of a nervous laugher than anything sadistic.

Both are the light side and dark side of Chara's character. However unlike Flowey who was a soulless being, Chara inhabited a being with a soul which was Frisk and hence he had the potential for good and to feel compassion for the characters (this is represented how the players felt compassion to the characters).

In the pacifist playthrough it was Chara's determination to liberate the monster that drove the game. During the final battle when interacting with Toriel's Lost Soul one of the dialogue was "You tell the Lost Soul that you have to go if you're going to free everyone. Something is stirring within her".  This reveals what Frisk actually said to Toriel (we had no way of knowing before the final boss fight with Asriel as Frisk was a silent protagonist) during the section in the ruins when Toriel was spared and Frisk left the ruins. It makes no sense for Frisk to say that as Frisk was a stranger who just fell into the ruins who never met the monster before. However this is consistent with Chara motivation who believed he was the future hope of monsters and humans as shown by the flashback either during death or sleeping in Toriel's house and was determined to exit the ruin and to free the monster kingdom. In a way this was a redemption of Chara's character. In the beginning Chara wanted to kill 6 humans to liberate the monsters but in the pacifist playthrough Chara ended up achieving the goal peacefully without anyone dying. After the pacifist run finish there was one final choice where Chara is place in a similar dilemma to Flowey. Chara can let go of Frisk and essentially rest in peace and essentially leave the mortal coil and let Frisk go or do what Flowey did and reset the world. If the reset option is chose then Chara would mimic Flowey choice as demonstrated by this quote 

"But as I left this mortal coil... I started to feel apprehensive. If you don't have a SOUL, what happens when you...? Something primal started to burn inside me. 'No,' I thought. 'I don't want to die!' ... Then I woke up. Like it was all just a bad dream"

In the genocide playthrough it was Chara hatred of humanity and lust for power that drove Chara's determination. Ultimately the end game of Chara was that it wanted to exit the monster world and destroy humanity. That's the reason why Chara asked the players to reset the game and do a (soulless) pacifist run so it can escape the monster kingdom and kill all the humans. Unlike the pacifist run, the genocide run strengthen Chara's determination as the lust for power is augmented by Frisk behaviour.

The reason why it was revealed the character was controlling was Frisk at the end of the pacifist run and not Chara was because that was the point where Chara's determination has been fulfilled. Asriel was liberated and he decided to break the barrier which liberated the monster. This completely fulfilled Chara's ultimate goal and hence Chara's determination has subsided as Chara achieved its goal. Contrast this to the genocide run where instead of resolving Chara determination we cement his determination by indulging in his anger and hatred and lust for power to an extent where he completely controls Frisk body (as shown by Chara name appearing when looking at the mirror). Once Frisk gets power, Chara becomes more determine for more power and hence reveal itself openly. In the pacifist run liberating Chara is just passively influencing Frisk to lead Frisk to liberate the monsters and to keep Frisk alive.

Now the rebuttal is how do we explain Chara becoming a separate character outside our control in the genocide ending. My view is that is part of the theme of Undertale. When you have the ability to time travel and essentially fix any mistakes you have done and have the ability to shape the world to your vision. A question pops up, is all the things we that we normally consider immoral and unethical such as murder really bad if you can just click your fingers and the consequences disappears? Flowey started to kill for that exact rationale out of curiosity knowing that Flowey was immune to consequences. However, the main theme of the game is that you can't click the fingers and erased the consequences even if you had the ability to time travel. If you were able to maliciously murder people (and to play the genocide run you simply can't argue self-defense for killing Papyrus or attempting to kill monster kid) and to commit genocide you have to irreversibly change your personality to do that. Once you cross the moral event horizon there is no going back and you simply can't go back to being a good person. This is represented in game where Chara became a separate being from the main character. We the player lost control because to kill all those monsters, we permanently lost control of our moral center and there is no going back. Chara determination in acting out his hatred goes beyond our player's control. So the player is Chara but the players determination to commit genocide cause a disconnect between the players and Chara where previously they were interconnected. 

Asriel could have been redeemed as he was soulless when he committed the evil act and we could call to his good side when he accesses to souls and compassion to redeem him. Chara couldn't be redeemed because Chara did all the activities while having access to soul (Frisk) and hence have the capacity to feel compassion. This is represented by how a lot of players felt bad for doing the genocide run and yet still went ahead with it. We had the capacity for compassion but ignored it and killed anyway. Having Chara becoming a separate entity that the player can't control represents that our own dark side once unleashed to do heinous acts can no longer be controlled. So that even if the players decided to do a pacifist run afterwards it all comes to nothing as once you unleashed your own dark side there is no return. There is no choice to be a good person again as need to become a bad person to indiscriminately kill sentient beings. Ultimately this leads to Chara stealing Frisk soul, escaping to the surface and destroying humanity.

So this is my theory on how Frisk, Chara and the players relate. Frisk was the body, Chara was the inherent determination/motivation driving the story and the player was controlling Chara until either Chara fulfilled his goal of liberating monsters or destroyed humanity.