Varys isn’t omnipotent, so it very much depends whether he gets an opportunity. It’s quite possible that Varys gets killed in the taking of the city, or the fighting disrupts his network, or the Red Keep burns to the ground, etc.
In a lot of your hypotheticals around the Battle of the Blackwater, the result seems to be ‘All Hail King Stannis’. But, even if Stannis had won the battle and seized King’s Landing, isn’t it likely that Varys would have had him killed, Kevan-style, to make room for Aegon?
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