Be Careful What You Wish For: Mai rides away on her motorcycle and thinks to herself that she hopes Joey can spare a thought for her even as their paths diverge again. He is thinking about her… and laughing from afar as he watches her bike flip over on the beach and give her a face full of sand.
Designated Hero: In-universe, Dartz is treated as if he's completely redeemed and sympathetic after losing his memories of being evil, which is rightly called out by the Pharaoh.
Easily Forgiven: Lampshaded at the end when Chris reveals she's Dartz's daughter and points out that him killing her probably should have been a bigger deal. Ironheart also says that Dartz is redeemed because his Laser-Guided Amnesia means he doesn't remember any of the evil things he did, which the Pharaoh objects to.
Tempting Fate: After being reunited, Yugi hopes that nothing will ever separate him and Yami again. The text then reminds anyone familiar with the source material that the next season is the final one and concludes with Yami leaving for good.
Unexplained Recovery: How Weevil’s comatose body ended up in the same hospital room as Rex’s is unexplained.
Wrong Genre Savvy: When Dartz starts giving his "As Long as There Is Evil" speech, the Pharaoh decides that means the final battle is conceptual and he can win by asserting faith in humanity. Then Dartz has his giant undead Leviathan eat him. Double Subverted in that the Pharaoh wins on a conceptual level anyway by showing that "evil can never overcome the power of sexy anime characters."
