I think the movie will distress people who are only familiar with the anime continuity. The end of the movie is clearly a reference to the end of Death-T, and that’s a powerful and uplifting message to conclude the series with. Because Kaiba does indeed return after Death-T, and he returns as a much better, kinder person.
If you read Death-T, it makes a lot more sense why Kaiba is so determined to rebuild the Millennium Puzzle. After Death-T, Yugi shattered Kaiba’s heart and forced him to rebuild it like a puzzle. If Kaiba was able to regain so much happiness from rebuilding the puzzle of his own heart, then surely rebuilding Atem’s puzzle would ease the grief of his passing. Of course Kaiba is mistaken in that respect, but he’s not crazy.
A lot of people are saying that Kaiba regressed in the movie, and that’s true to some degree. Seto is very human in that regard, because who wouldn’t regress after the death of their best friend? But he isn’t acting out of malice and anger like he did in Death-T and to a lesser degree in Battle City. He just needs closure. And I think Kaiba progressed in other important ways, such as being open to a friendship with Yugi.
In my opinion, Seto leaving Mokuba at the end of the movie shows how far the two have come. Mokuba has also grown since Death-T and Duelist Kingdom, he’s not a little kid who’s going to get kidnapped again. Seto can leave KaibaCorp in Mokuba’s care and trust that everything will be alright even without him there. That’s a big change from Death-T when Seto called Mokuba a loser and a failure. Mokuba never wanted Seto to be his surrogate father; Mokuba wanted to be respected by his older brother and entrusted with adult responsibilities.
Sometimes I get the feeling that the anime completely misinterpreted Seto and Mokuba’s relationship. Although Seto might be the older brother in chronological years, it’s Mokuba who actually takes on the responsibilities of the older sibling. After Death-T, Mokuba realizes that Seto can hardly take care of himself much less his younger brother. In the manga, Mokuba isn’t waiting around to be rescued by Kaiba. Mokuba is the one who’s trying to protect his older brother.
And that’s okay because the Kaiba brothers don’t live in a vacuum. Atem might be Seto’s rival, but it’s Atem who becomes Mokuba’s mentor and big brother figure. (Yugi and Anzu also act as role models to Mokuba.) Mokuba can take on the responsibility of protecting Seto, because he trusts that Atem and the others will be there to protect him.
There first meeting at the Duelist Kingdom is a tentative trust, but Mokuba’s worldview is shaken when he realizes that Yugi kept both his promises. Not only did Yugi save Mokuba and KaibaCorp, but he was also right about Seto’s recovery.
So in the end, Mokuba acts with bravado in front of Seto, but he still convinces his brother to act kinder toward the nerd herd. Duelist Kingdom sets the stage for Battle City.
Duelist Kingdom sets the stage for Battle City. At this point, Mokuba is finally willing to stop submitting to his brother’s demands and actually challenge him on his poor decisions.