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If you want to experience the historic duels as they were played out in the anime series, you should use the Story Deck for the campaign.
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Use a User Deck instead of Story to progress faster
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They're just good to have in general, for everyone. While you need to have a strong theme for a good deck, always make sure to have some staple cards too. These are cards that will always help you out in a pinch, give you control of the board, help you go through your deck faster so you can get the cards you want, etc. A few of these cards would be "Dark Hole," "Raigeki," "Harpie's Feather Duster," "Pot of Greed," "Solemn Judgement," "Mirror Force," and more.
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Staple cards are basically cards that can fit in any deck, regardless of theme or type.
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