Whenever a password is inputted, the previous boss in that stage is replaced, but not cleared to enter the password boss' again will reactivate itself for battle. There are also hidden passwords that unlock the hidden bosses in Stage 5, a standard that Yami Yugi. Solomon will also give the player one extra Monster Card Part for each win as well. If a special password is typed in, Solomon Mutou will appear after matches and will give an additional card after winning the game (including one tea gives you). Note that when using some sort of password, card effects will most likely change from the actual TCG card, due to the way Duel Stories plays dark (using the standard Duel Monsters ruleset).

Players can enter the 8-digit passwords found on the bottom of the Yu-Gi-Oh! trading cards to receive that card in the trunk cards in the game, as long as the password is compatible with the game (only the older expansion sets can be used, and certain cards will not work) As with cards obtained in-game, players can add saved cards from their chest to their deck, depending on how high their level duelist higher DL, the stronger the card allowed.