- One shot, seen in most trailers, is of Yugi glancing down at his deck with a resigned expression before hugging it close to his chest. It parallels◊ a similar shot◊ of Yami Yugi from Yu-Gi-Oh!: Bonds Beyond Time.
- The shot in question is from when Yugi, Joey, and Tea are walking home from school. Taking out his deck, Yugi admits that despite having moved on he still misses Atem. It's implied that Yugi rarely duels anymore because it just isn't the same without him.
- After Battle City, Kaiba compared dealing with his grudge against Gozaburo to playing a Shadow Game and wondered what he'd do once his past is buried, staring at his locket of Mokuba while remembering his wish to build amusement parks as a child. While sad enough on its own, it's made worse with this movie having Kaiba regress to obsessive levels in his desire to defeat the Pharaoh, his dreams for the future forgotten.
- Seto Kaiba cannot get over the fact that the Pharaoh has gone on to the afterlife, denying Kaiba the chance for a definitive rematch and a chance to defeat him. The opportunity to find the Pharaoh is Kaiba's sole driving motive, and he spends the entirety of the six months between the original manga's ending and the movie itself, as seen in the prequel manga, doing nothing but trying to find him no matter the cost.
- He nearly breaks down when Yugi completes the Puzzle and shows him it won't bring Atem back. He looks on the verge of tears.
- Even though he turns out to be right, there's something incredibly tragic about Kaiba's denial. He is a teenager and he and his brother had a frankly traumatic backstory. Now he seems incapable of interacting with the world in any healthy manner. His behavior in the movie is highly unhealthy, but he's just reacting the only way he can to the loss of the closest thing he ever had to a friend.
- There's a moment just after that speech when Kaiba plays the card Monster Reborn, the very card Yugi made a point of not playing in the Ceremonial Duel against Atem. Yugi moved on. Kaiba couldn't.
- Particularly bad since the movie seems to follow the canon of the manga more than the anime. In the manga Kaiba wasnt there for the Ceremonial Duel. Unlike Yugi and the others Kaiba never got to say goodbye.
- Kaiba's manic behavior in Transcend Game has mutated into a driven, desperate grief in the movie. At one point he talks about the realm of the physical being a prison - that is, a barrier that separates him from Atem.
- Sera, Aigami and Mani's backstory as a poor gang of orphans just trying to survive with an abusive caretaker.
- Early in the movie, Yugi and his friends are talking about their dreams for the future. Yugi, Anzu, Jonouchi, and Honda all say what they'll be up to after high school, but despite Ryo being there he doesn't say what his dream is and they don't ask him.
- There is also Honda/Tristan's situation. Everyone else can choose their futures, but he is basically left no option but to work in the factory like his father. He has no choice for his future.
- Yugi and Atem's final duel, while already sad, becomes even worse when it's revealed Kaiba became determined to find and reassemble the Puzzle to duel Atem and Aigami and the Plana's powers activated upon the Pharaoh's departure, leading to the events of the movie. It turns what was a bittersweet, powerful moment for Yugi—defeating his other self and standing on his own—into a tragic one, because in doing so Yugi almost doomed the world without even realizing it.
- And on a personal level, it makes the final scene of the manga fairly heartbreaking. The second-last page shows Kaiba and Mokuba were outside the temple, but it's unclear whether they were there the whole time or had just arrived, leading to a big question. Was Kaiba's obsession borne from getting there too late, or from being too scared to say goodbye?
- Ryo Bakura's entire situation. Aigami forces him to have a flashback to how he got the Millennium Ring. He got possessed by the Ring when he was four years old and had it fuse into his chest, leading to Dark Bakura killing Shadi and Ryo's father, and Aigami wants to kill him for the incident. Ryo mentions not wanting to talk about the Ring at all and suffers headaches when pressed, becomes trapped in another dimension for the last third of the movie, and has the Ring itself drive Aigami and Mani to kill him.
- And his response to Aigami all but torturing him? He apologizes for the pain Aigami has suffered, because he knows what it's like to lose those he loves.note We finally find out what happened to Bakura in the first place and how much nothing that happened was really his fault.
- The very last scene of the movie, where against Mokuba's wishes, Seto breaches through to the afterlife and prepares to duel Atem. He has Aigami's Quantum Cube, but the movie leaves it up in the air as to whether going to the afterlife made him dead as well, and whether or not he'll win against Atem when he finally duels him. Complicating matters further is that he leaves KaibaCorp in Mokuba's hands, suggesting he may not return right away, if at all.
- The ending theme in the Japanese version, To Believe in Something, seems to be about Kaiba's relationship with Atem. The fact that it comes after Kaiba enters the afterlife to duel him makes it sadder.
- It could also be seen as Yugi's relationship with Atem, Anzu's relationship with both Yugis, Mokuba's relationship with Kaiba, or even the fans' relationship with Yu-Gi-Oh as a whole, as this is likely the last time continuations of the original story will be made.
- When Joey is trapped in the alternate dimension, about to disappear forever, he doesn't think of his little sister, Serenity to give him strength. Even sadder is that she doesn't appear in this movie at all.
Tear Jerker / Yu-Gi-Oh! The Dark Side of Dimensions