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At the end of Here Comes the Flood, Black Magga will have a ton of cards under her. What happens to these cards at the end of the scenario. Are they banished or just returned to the box? What about the allies under the scenario if I fail? Are they banished? It's important because Basic cards could be removed from the game
They are just simply "put back in the box". Lacking any other instruction, that is the status of all cards when the game end. See page 19 (I believe) if the rulebook.
This is the part from page 19 I was referencing:
Once you’ve completed a scenario, whether you win or lose, rebuild your character deck (see Between Games, below). Put all other cards back into the box.
So since nothing else tells you to Banish the cards Black Magga ate, they are subject to this rule.