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If I'm attacking with Nemesis Prime and in the course of my attack burn through my deck, his ability triggers and I shuffle. Once done shuffling, the bottom card goes under him. Does he instantly get the +3 attack, or does it get added to his next attack?

He gets the +3 attack instantly.
Source: Wizards of the Coast (2019-01-25)    【Link to Ruling】
Tags: Nemesis Prime, Dark Clone, Nemesis Prime, Dark Clone