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Rule #1: If a Pokemon faints, it is dead.
Rule #2: Only attempt to catch the first Pokemon you see in each area
#2a: Dupe clause (double-edged: may not catch dupes)
#2b: Baby clause (only first form pokemon count as a sighting; pokemon who gained an earlier form in later gens still count as first form; Marill and Azurill are catchable, Azumarill is not.)
#2c: Shiny clause
#2d: Spearow clause (Spearows do not count as a sighting and may not be caught. They must be killed. All of them.)
#2e: Gift pokemon are free catches; they do not count against the catch for the area.
#2f: The Johto Safari Zone may be entered three times: once to catch a Sandshrew for Baoba and twice more after unlocking all of the areas and objects. The Sandshrew may not be used in combat. One all three visits one pokemon may be caught (Sandshrew doesn't count) and it need not be the first one seen. 
Rule #3: Fly may be pokesav'd on to pokemon who cannot normally learn it, as it is only used for comic-making purposes.
Rule #5: If TRUMP CARD the Lugia faints in the game, Candace dies in the comic.
Rule #6: Trading is allowed for evolution purposes only.