Nuzlocke Rules and Notes:
First thing's first: I believe a nuzlocke is better portrayed in comic form, but since my drawing is average and I don't have the time to draw everything, I'm writing it first so I can at least continue my story.
Now that that's out of the way, time for my nuzlocke rules for Johto:
You can only catch the first pokemon you run across in each area.
This rule doesn't take effect until you have the ability to catch pokemon
If a pokemon flees battle, you can have one more chance in that area. Just one.
The Bug Catching Contest is deemed a different area from the National Park it takes place in.
The pokemon needed to pass the Safari zone doesn't count, but must be released as soon as you pass. Once the test pokemon is caught, rule 1 activates.
The only legendary you can catch is Ho-oh, and this is only if you don't run into any pokemon in the tower beforehand.
Only Repels found in the wild can be used
Should a pokemon faint, it is considered dead and will be boxed permanently
Should you find a revive in the wild, you may use it on fainted pokemon IF AND ONLY IF it is used during a battle and if it's the same battle as the one the pokemon fainted in. Ergo, you must risk another of your pokemon to bring it back.
All pokemon must be nicknamed