Rules:
1. You can only catch the first Pokémon in each area.
--> Duplicate clause: You can't catch Duplicates, ever. The Pokédex entry counts. (Say you caught a Pidgey, but it died before you could evolve it. You meet a Pidgeotto, you don't have a Pokédex entry and you can catch it. But if you did evolve it and it died then, you can't catch the Pidgeotto.) In a case you encounter a duplicate, you may search for alternatives, but only five encounters long.
--> Legendary clause: You may catch Legendaries if required, but can't if it's not. You can't use them in battles, period.
--> Miss clause: If you don't catch a Pokémon you could catch, you're out of luck.
--> Shiny clause: If a shiny is not your first encounter, you're out of luck.
--> Trade clause: You may trade a Pokémon in-game, but it must be a first encounter. You may not trade outside the game and can never evolve Pokémon who require trade for evolution.
2. If a Pokémon faints, it cannot be used in battle ever again.
---> In the Comic, Pokémon who fainted while in a to-death challenge are dead. Even those who are not in a to-death challenge are to be gotten rid of in any way.
--> If all your Pokémon faint, you are allowed to take any number of boxed Pokémon and continue your journey.
3. Battle style is "set".
4. You may only buy 10 Items per town or other area where you can obtain items.
5. Because the Plot is more relevant than the game, 3 Pokémon may be "revived", i.e. even though they fainted, you may pretend it didn't happen. Use those wisely because you will not get more than 3.
6. For reasons of self-control, you must state in the comments of each part what happened in-game, especially concerning rule 5.