Masterplan is a Shadows artifact that you put another card from your hand under when you play it. You can then later play that stored card as an omni effect (sacrificing Masterplan in the process). My question is, what becomes of the stored card if Masterplan is destroyed, returned to your hand, or archived from play? It seems reasonable to me that with any case the stored card goes to your discard pile, but it could be just as true that the card follows the Masterplan to where it was sent (discard pile, hand, or archive). Which would it be?

The card stored in Master Plan is only connected to it while its in play. It will go to the discard reguardless of where Master Plan goes except when you use it omni ability. Nothing purge or archived it which is the only way something can end up in either of those states. And you can only get it into your hand from drawing it so it can’t go back to your hand.

The discard pile should be the only place it could be since that would be the only place it could go from not being played.

Since no rule covers what happens to the card under Masterplan, CLEARLY it must be left face down where it was and never touched again. It can never be restored to the deck and is lost forever. Even if you go to play a new game, you must leave the card there! : - )

But in the absence of any RAW or rulings, common sense suggests it goes to the discard pile.