You know how Atem just kinda chilled and did whatever during Duelist Kingdom and didn't know who he was and didn't even question it? Not until like after Yugi stopped him and confronted Pegasus after and learned about shit?
And given the time difference of s0 and DK...Atem was legit clueless for a whole year. He thought he was Yugi for a whole year. (If you base off anime anyways.)
What...like, how did those two interact during that? Like...they were kinda aware, but they didn't know how to explain it and just kinda went with they were two sides of the same person?
In manga, basing off of Yugi's thoughts and such, I think he was aware that Atem was...someone else? But he didn't know how to explain it or what to think? At least for a long time he didn't. Yugi is very smart and kinda figured things out once he is given more information.
But still, the overall question here remains...how the hell did the two perceive each other for that whole fucking year? Thinking they are one and the same but have a feeling they aren't?
Can you just...imagine the pure frustration and fear Yugi went through? He so badly wanted to try to talk to Atem (I don't believe for a second Atem couldn't hear him in all attempts) but he just...didn't respond? He was literally forced aware that his control can be ripped out of his hands once Yugi stopped him in his duel with Kaiba. And had to face the fact it could be, but it can be done in a POSITIVE manner. Called cooperation.
My personal hot take: Yugi was hella lot more aware and able to see what was happening once he realized someone was taking over his mind when in danger. Very early on. He got more and more practice, and he wanted to talk to this stranger inhabiting his mind...but grew very fucking scared when he saw the lengths that Atem would go to win a game (though in fairness, Atem felt very pressured and left with no choice, but not justifiable).
Yugi and Atem felt very similar in emotions when it came to the previous duels...anger, confidence, etc. I would even say Yugi agreed in some cases of Atem's...behavior and opinion. And when he didn't, he couldn't reach him or was blocked off somehow. But their friends were safe and happy, so couldn't be all bad.
Duel with Kaiba happens, and the finals happen. Time to reach Pegasus. Now THIS...is where things become interesting.
I want to say Atem, for once, was the one adamant on avoiding Yugi's presence. Intentionally this time. Duel with Mai happens, and this is the first time they really become in sync...at least in spirit. The duel with Pegasus is where the first time to actually talk to each other happens. They have experienced so much shit together already but could have never talked...they know each other, but also not really?
Hence the excitement Yugi has when Atem fucking finally decides to rely on him and work together. And this is where Atems genuine over protective habits over Yugi began to develop. At first it was just to make sure himself (or what he thought was) and friends didn't get hurt, but...him and Yugi connected in a way no one else could before that day. It's important and sacred and needs to be protected.
I am curious to anyone else's thoughts if you have any!