Actually I’m just gonna go ahead and do a full post about this.

“Season Zero Atem murders people for being mean to Yuugi” is a fanon construction because there are inaccurate ideas behind it.

The first is that Atem just goes around murdering people. It is true that he kills two people in the early manga, both times by setting them on fire. But it’s hardly a regular thing, and at least with the Burger World incident, there wasn’t a whole lot of options when an unstable criminal is holding your friend hostage and a gun pointed to your head.

The second is that he does his penalty games over pretty much nothing. Not really. It’s more than just “being mean” - usually assault or imminent danger is involved. In the cases where there isn’t, the punishment tends to be light or non-existent (such as the Love Tester thing being taken away - the teacher’s only punishment was getting revealed to be bald).

The third, and I think the most common misconception, even among people who recognize that the first two are inaccurate, is that he does this in defense of Yuugi. He actually very rarely acts when only Yuugi has been harmed (the only time I can think of off-hand is the Monster Fighter incident…but even then, the villain was stealing from other people too). For instance, the punishments that resulted in death? BOTH of those were on account of Anzu, not Yuugi. Yes, Yuugi did get hurt in the second incident, but it was because of Anzu crying that Atem took over, not because Yuugi got hurt.

This isn’t because he isn’t protective over Yuugi or that he doesn’t want to defend him. It’s because he believes himself to be Yuugi - and Yuugi doesn’t consider himself getting hurt to be a great offense, not one great enough to distress him to the level needed, at least. Yuugi, subconsciously early on, and consciously later, has control over letting Atem take over. Atem can’t just force his way out - Yuugi has a clear reaction to a friend getting hurt or to immediate danger, and the Puzzle shines and Atem takes over as a reaction to Yuugi’s extreme distress, that doesn’t happen when Yuugi himself is being hurt. We can even see Yuugi repress that from happening even when he is experiencing those feelings of extreme distress - most notably during Death-T.

I think this misconception comes from a combination of a few places. The first is that I think a lot of people who buy into this haven’t actually read the manga and maybe even haven’t watched the Toei anime. Nothing wrong with that, but it does give a skewed perception because their knowledge of that part of canon is secondhand and lacking context/nuance.

The second I think is shipping lenses. Puzzleshipping is one of the most popular ships, if not the most popular ship, in the fandom. And not without cause, of course - it’s a very sweet ship and one I like myself. And the fandom is going to find the idea of defending someone to that extent very romantic, so they create that fantasy and fanonize it to the point of believing it to be canon.

There’s also, I suppose, an aspect of the simplification/flanderization of characters as well, in this case Atem, that could be a part of it. Early manga Atem gets reduced to “crazy murder guy” because that’s easier to poke fun at, easier to digest, easier to keep track of, etc…rather than considering all the nuance and personality of his early character as a full character and not just a plot device to punish the villain of the week.