With none of my own creatures in play I cast Smallpox discarding Bloodghast from my hand and sacking Flagstones of Trokair to it. Does Smallpox resolve then Flagstones trigger thus finding me a Plains and bringing my Bloodghast to the battlefield? What is the order in which things happen?
Actions are carried out in the order written on the card. You will lose a life then discard a card then sacrifice a creature and then sacrifice a land so by the time you sacrifice a land the Bloodghast will be in your GY. Note that Flagstones of Trokair has a triggered ability when put into the GY and triggered abilities will always wait for a spell or ability to fully resolve before they themselves will resolve.
You follow a spell's instructions "in the order written" (C.R. 608.2c); however, this order doesn't make any difference in this scenario. This is because while a spell is resolving, no other spells or abilities (such as the triggered ability of Flagstones of Trokair) can resolve; rather, any abilities that trigger during that time will go on the stack after the spell finishes resolving (C.R. 116.3b, 116.5). (See also this thread.)
A better example of a case in which Smallpox's order of effects matters is if we replace Bloodghast with Centaur Vinecrasher. Here, since you discard a card before sacrificing a land, Centaur Vinecrasher will be in the graveyard in time for its last ability to trigger from Flagstones of Trokair going to the graveyard.
Bloodghast and the Flagstones enter your graveyard during the resolution of Smallpox. Smallpox is then put into your graveyard. Then the triggered ability of Flagstones is put onto the Stack.
When the Plains enters the battlefield, Bloodghast, being in your graveyard, triggers.
In this case, what matters isn't when Flagstones triggers, but when that ability resolves. If they're not mana abilities, abilities use the Stack and give the opportunity for response to all players.
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If you so choose, yes, since it is a may trigger. Bloodghast has its own triggered ability that functions from the graveyard, and luckily for you, it is in that zone when the Flagstone's trigger brings in a Plains, so it triggers, and when that trigger resolves, you may return to Bloodghast to the battlefield.
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A better example of a case in which Smallpox's order of effects matters is if we replace Bloodghast with Centaur Vinecrasher. Here, since you discard a card before sacrificing a land, Centaur Vinecrasher will be in the graveyard in time for its last ability to trigger from Flagstones of Trokair going to the graveyard.
When the Plains enters the battlefield, Bloodghast, being in your graveyard, triggers.
In this case, what matters isn't when Flagstones triggers, but when that ability resolves. If they're not mana abilities, abilities use the Stack and give the opportunity for response to all players.
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