Destroy refers to an act that results in sending a card to the Graveyard, either by battle or by card effects (that use this term), or sometimes due to game mechanics or an effect that doesn't allow a card to exist in specific Zones.

Usually, cards in the Main Deck and Banished Zone cannot be destroyed.

Not all cards that send cards from the field to the Graveyard destroy them; cards like "Dark End Dragon", "Ninjitsu Art of Super-Transformation", "Number 50: Blackship of Corn", and one of the effects of "Number 7: Lucky Straight" send cards from the field to the Graveyard, but they do not destroy the cards, since they don't include the word "destroy" in the text, so these effects cannot be negated by effects like "Stardust Dragon", and other similar effects.