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I guess that would depend on the SA. If it said "shuffle EC into deck," then the "shuffle" part would target the deck. If the SA said, "Return an EC to deck and shuffle deck", then the EC would still return to deck.
JT allows shuffle.
Can you affect something that is protected by targeting something else?
So, if your Priests from the House of Eleazar are protected from discard abilities, and your opponent discards your Goshen which happens to be holding a Priest from the House of Eleazar, you're saying that the Priest would not be discarded because they are indirectly protected? Is that the scenario you are looking for?
This will take some debating.
To get a ruling. As of now I would have no idea how to rule it.
I would think that if my deck is protected, even though I am targeting the character, you can't do it, because it indirectly targets my deck by adding to it.
My thinking (just throwing this out there) is that the card being returned to deck is not a part of the deck until it is a part of the deck - i.e., when the return ability has already completed. The return ability does not target any of the existing cards in the deck, and by the time the returned card is a part of the deck and therefore protected, the ability has already completed.
Scribe's ability has 2 targets, the OT enhancement in the discard pile and the deck where it will bottomdeck the enhancement. If Thad is protecting the deck then it cannot be targeted by Scribe.
Then wouldn't anything that bottom decked something have two targets?
It seems to me that Ahimelek the Hittite is targeting the Evil Character and the owner's hand, however, based on the Grapes of Wrath ruling with Simon the Zealot I'm probably wrong.