The prequel manga
- Seto seeing not only Atem, but Kisara's spirit in the next dimension.
- Mokuba shutting down the power when he sees Seto's life is in danger.
The movie
- Atem and Yugi's team-up and brief reunion.
- There are a couple Yugi/Anzu moments throughout the movie, with them being physically close and a Held Gaze before high-fiving.
- Yugi trying to help Kaiba by stopping their duel to show him what will happen when the Puzzle is complete.
- There's a blink and you miss it shot of Yugi's face after Diva divulges his backstory and insists on duelling to the end. Yugi doesn't look angry at Diva, but sad, showing compassion for Diva even as he disagrees with his methods.
- Atem's elevation to Big Good status, using his powers to help the gang from the afterlife twice. There's a still of him gently smiling at his friends.
- The scene is from after Atem defeats Dark Diva and he and Yugi have separated into two again. Both of them stare at each other smiling happily.
- 4K Media held a voiceover contest for fans to voice characters in the dub.
- Yugi tells Kaiba that not only will he duel Aigami, not him, the only reason he's doing so is for Bakura's sake.
- When Atem appears and delivers the finishing stroke, out of all the gods and monster cards he could have picked he summons Mahad, maintaining the theme that friendship is valuable.
- And when Mahad is summoned, he appears kneeling in front of Atem, rather than facing the enemy. It really drives home just how loyal Mahad still is to Atem, even after all this time.
- After spending the whole movie being an obsessive jerkass, Kaiba does show some positive character development in the end - he asks Yugi to team up with him to fight the final boss and sacrifices himself during it having full faith that Yugi would find a way to reach Atem and defeat their foe. Yugi even compliments him for having faith that Atem would return to help them when he himself didn't, and they part amicably.Kaiba: You have your bond with him, and I have mine.
- In the Japanese, too. The script is slightly different and has Kaiba using Atem's catchphrase.
Kaiba: Are you sure about that?- The ending where Kaiba goes into the afterlife to find Atem (assuming Kaiba returns). Atem greets him with a smile, and the movie just ends there, rather than on any duelling or snarking between the two. It's probably as close to an understanding of friendship as Kaiba has ever gotten, and the ending theme in the Japanese drives the point home that whatever happened between them in the past doesn't matter considering the bond/rivalry they've formed since.
- Sera and Aigami smiling together in Egypt, seemingly at peace at last.
- The last spoken line in the movie before the epilogue, and Yugi's last spoken line in general, is "Goodbye. And thank you." It could be the movie breaking the fourth wall so Yugi could thank all the loyal fans of the show for following along for all these years.
- Many fans echoed this line following the tragic death of Kazuki Takahashi in July 2022.
