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There's a mountain of implications that Kris is being controlled by the player's soul. I'll start with Chapter 1 evidence.
When you return to the overworld in Chapter 1, we learn that Kris can play the piano, but when you try it, it goes poorly. And other characters make some minor notes that Kris seems different from usual. Sans saying they had never met has a wink to go along with it, and most people seem to think that Sans is implying they have met before. It'd make sense if he was doing that because of the soul residing within Kris, not Kris himself, but that is a bit more of a stretch. It's also more logical for the player to be able to move their soul so freely like that. But most of all in Chapter 1, the biggest thing is the opening sequence. We see the red soul appear at the start of the game, and the red soul is tasked by an unknown being (most likely Gaster) to create a new vessel for themselves to inhabit. But at the end, the original entity speaking to them is cut off (it isn't the same one that was having you make a vessel), the first speaks in all caps and the second is more natural, and the second one has a different typer value (meaning a different "voice"). And that's followed by Kris "waking up". It's clear that what happened is you weren't allowed to choose an empty slate for yourself, and you were sort of "thrown" into Kris's body. It's also very weird how Kris can rip "his" soul out and throw it into a birdcage without dying.
In Chapter 2, we get even more instances of characters saying that Kris's behavior is unnatural, @Imaginym has already mentioned a lot of the Chapter 2 evidence as well. Such as, when Kris calls for help from Susie or Ralsei, nobody comes, but when the option for Noelle is chosen, it says "You" called for help, and almost immediately, Noelle defeats Spamton. That makes it literally almost guaranteed by itself that Kris isn't really the one doing all of this. And another thing is the scene that happens after the standard Spamton NEO battle. Kris seems to be highly uncomfortable and is even yelling when he speaks to Susie and Ralsei. I think I know why. Because Spamton was a puppet, being controlled by some higher entity. The literal one and only thing he desired was to be free, but in the end, freedom wasn't possible to obtain. I think the reason Kris is so mortified is because he knows he's being controlled as well, and in that scene, we see a little bit of how Kris is feeling. It also matches up with us controlling Noelle to the point of mind control. She barely realizes she's being controlled, at most she thinks Kris is just influencing her, not literally manipulating her thoughts.
Now, originally I thought it was Kris pulling you out of his body at the end of Chapter 1, but seeing as when that happens again in Chapter 2, "Kris" seems to have bad intentions. Slashing Toriel's tires and creating a new Fountain, which is literally trying to destroy the world. Unless Kris has an ulterior motive, that most likely isn't Kris, meaning there is another being controlling Frisk we don't know of. I believe currently that it's Chara, but it could be wrong.
