Yeah, I think his story is pretty tragic in a lot of parts. Especially the whole being trapped in a puzzle for 3000 years because he deliberately did that to himself, and that part just makes me really emotional. We don’t know exactly what happened the first time around or how he came to the conclusion that this was the only way he could stop Zorc, but just the fact that he willingly gave up his own name and all of his memories, his very identity and everything he ever was, gave up his chance to go to the afterlife after his death just to protect his people. That’s just such an amazing and heartbreaking thing for someone so young to do, and it’s no wonder why so many people worked so hard to try and ensure he would get to the afterlife in the end.

I think his time alone in the puzzle also had a rather profound impact on him in the present, not just in the way he was when he first emerged but in a more long lasting way. It’s not something he ever talks about really, but I think his fear of losing and being alone comes at least in part from all those thousands of years of solitude. We saw over and over again throughout the series how he has a tendency to freeze up and start doubting himself when he truly thinks he’s going to lose and how he loses his confidence when he thinks that he’s alone. He often has to be reminded that his friends are always with him no matter what, and that even if they can’t physically be there that they’re still there in spirit at least. And I think this comes from that time of solitude, because he’s not used to having friends and obviously doesn’t remember having them in the past and so he often feels like he has to be the one to handle things himself. But he’s not really strong enough to be able to succeed alone. His true strength comes from the fact that he fights for others, not just for himself. He’s always trying to help his friends to the best of his ability and protect them because it’s something he feels he needs to do. Which I think some of that probably comes from the time when he was still operating off of Yugi’s emotions and perhaps a bit of it is an echo from the past, not a memory but just a feeling that he wants to protect others. So basically he was just a really lonely kid when he reawoke who really wanted to have some friends.

And then there’s his acceptance of the accusations that Yami Bakura and Marik put onto him even though he wasn’t the one who actually did anything to him. I wish the show would have gone into a bit more depth on how he felt about what Marik said about him especially. He does wonder several times what he could have done and what kind of person he must have been in the past and it’s brought up again in season 4 as well if I recall correctly. He never really tries to deny it though, because he has no idea whether it’s really true or not, and just accept that burden that Marik places on him without argument. His attitude is kind of like “You can throw any accusation you want at me, I can take it. But don’t you dare touch my friends because of what I might have done.” In fact that’s pretty much what he basically does say in that awesome scene after Mai’s duel.

And he does the same thing with Bakura as well. When he finds out about what happened in the past, he still accepts that responsibility as his own even though technically what happened to Bakura’s people was all Ahknaden’s fault. But Atem is pharaoh and thus feels it’s ultimately his responsibility as well and burden to take on, regardless of who is actually to blame.

I wouldn’t say that he’s all alone again at the end of the series though. We saw all the spirits waiting for him on the other side of the door, after all. And even if it wasn’t an entirely accurate depiction since some of those people had been reborn in the modern world, his father and mother would certainly be there on the other side with him at the very least. Ahknaden would be too, and hopefully he would no longer be crazy. And Mana would be there too since there’s no indication that she ever merged herself with her ka in the way that Mahad did. So he would definitely have plenty of company in the afterlife. And this is just personal headcanon, but I like to think that eventually when their lives have come to an end that Yugi and the rest of his friends will be reunited with him in death and they can all be together again for the rest of eternity.

I agree that it would have been nice if there had been some way that he could have lived on in the present and gotten a second chance to live out life like he was never able to, but I think that ultimately he still got a happy ending anyway.