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They also periodically add event stories to be viewed ingame at any time even if you weren't there for them, key word being periodically. They're never really gone forever until the game gets EOS'd.

Incidentally on that note, when you unlock Rebecca, Yugi and Atem have a conversation about Bonds Beyond Time that outright confirms the manga and anime versions of DM being separate universes, and them "combining" with their anime selves