Plot is something to do with Johto wanting to secede from Kanto and have its own independant league. Central conflict would be between those who support the notion (Seceders) and those who reject it (Indigoists). The New League is the result of that.
(Top row, from left to right, is 13, 5, 2, 1)
1 - Sundew Town
-> Route 51
2 - Merbau City
3 - Mahogany Town
4 - Ecruteak City
> Route 49
> Route 50
5 - Cypress City
...
6 - Olivine City
...
7 - Blackthorn City
8 - New Bark Town
9 - Cherrygrove City
10 - Violet City
11 - Azalea Town
12 - Goldenrod City
...
-> Route 52
-> New Victory Road
13 - Firlas City/New League
...
14 - Cianwood City
...
15 - Indigo League
=====
Mahogany Gym: Leader Pryce (Ice)
>Swinub, Sneasel
Ecruteak City Gym: Leader Morty (Ghost)
>Misdreavus, Haunter
Cypress City Gym: Leader Will (Psychic)
>Drowzee, Espeon, Xatu
Olivine City Gym: Leader Jasmine (Steel)
>Magnemite, Skarmory, Steelix
Blackthorn City Gym: Leader Clair (Dragon)
>Dratini, Dragonair, Kingdra
Violet City Gym: Leader Li (Grass)
>Tangela, Sudowoodo, Sunflora, Victreebel
Azalea Town Gym: Leader Bugsy (Bug)
>Parasect, Shuckle, Forretress, Scizor
Goldenrod City Gym: Leader Whitney (Fairy)
>Wigglytuff, Granbull, Togekiss, Clefable
=====
Firlas Tower First Floor: Elite Four Chuck (Fighting)
>Hitmontop, Heracross, Machoke, Poliwrath, Primeape
Firlas Tower Second Floor: Elite Four Falkner (Flying)
>Dodrio, Noctowl, Jumpluff, Farfetch'd, Pidgeot
Firlas Tower Third Floor: Elite Four Brooke (Water)
>Politoed, Mantine, Octillery, Qwilfish, Kingler
Firlas Tower Fourth Floor: Elite Four Terra (Ground)
>Donphan, Gliscor, Quagsire, Marowak, Sandslash
Firlas Tower Fifth Floor: Champion Karen (Dark)
>Umbreon, Vileplume, Honchkrow, Yanmega, Houndoom, Tyranitar
=====
Bonus Battle: Pokemon Trainer Silver (Various)
>Meganium, Slowking, Magcargo, Crobat, Blissey, Sylveon
>Typhlosion, Slowking, Exeggutor, Crobat, Blissey, Sylveon
>Feraligatr, Exeggutor, Magcargo, Crobat, Blissey, Sylveon
