Pallet Town is the very first place the player will be in. It is the only Town/City without a Pokecenter. Rival Gary and the player's house is located here. This is also where the player receives his/her first starter. Upwards is Route 1 and Viridian City.
Viridian City is right after Route 1 and is where the final Gym is located. The Gyms Leader's name is Giovanni and he specializes in -type Pokémon. Once you defeated Giovanni you get your 8th badge, the Earth badge. Giovanni is also the leader of Team Rocket that you'll come across at Lavender Town. On the left is Route 22. In that Route there is your rival, Gary, and a guard blocking you from entering to Victory Road (the guard will let you enter Victory Road if you have all 8 Gym badges). Upward is Route 2, Viridian Forest and the next city which is Pewter City.
Pewter City is where the first Gym is located. The Gym Leader's name is Brock and he specializes in -type Pokémon. Once you defeated Brock you get your first gym badge, the Boulder badge. After Pewter City is Route 3, Mt. Moon, Route 4 and then the next city, Cerulean City.
Cerulean City is where the second Gym is located. The Gym Leader's name is Misty and she specializes in -type Pokémon. After Cerulean City is Route 5, Route 6, and then the next city which is Vermillion City.
Vermillion City is where the third Gym is located. The Gym Leader's name is Surge or, preferably, Lt. Surge and he specializes in -type Pokémon. After Vermillion City is Route 11, Route 12, and then the next location which is Lavender Town.
Lavender Town is where Pokémon Tower is located. In it you can find a few -type Pokémon, Gary,Team Rocket with Giovanni at the top floor and the Legendary Pokémon Giratina (you need to be Champion for Giratina). After Lavender Town is Route 10, Route 7, Route 8, and then the next city which is Celadon City. Also you CANNOT Travel through taxi because they're too scared.
Celadon City is where the fourth Gym is located. The Gym Leader's name is Erika and she specializes in -type Pokémon. Celadon City is also where you can get a free Eevee from the house by the fountain. After Celadon City is Route 16, Route 17, and the next city which is Fuchsia City.
Fuchsia City is where the fifth Gym is located. The Gym Leader's name is Koga and he specializes in -type Pokémon. In front of the PokéCenter is Seafoam Cave where there are a lot -type, -type Pokémon and two Legendary Pokémon, Articuno and Kyurem (you need to be Champion for Kyurem). After Fuchsia City is Route 17 and the next city which is Saffron City. You can also get to the Mausoleum of Origins from here by defeating Kentucky Smith, an old gym leader (You need 8 badges).
Saffron City is where the sixth Gym is located. The Gym Leader's name is Sabrina and she specializes in -type Pokémon. On the left of the Gym is what used to be a -type Gym before Sabrina took over. There is no -type Gym Leader, but there are 4 trainers and 2 of them gives you either a Hitmonlee or a Hitmonchan depending on which one you fight. In the PokéCenter is Professor Oak and he will give you a Legendary Pokémon, Heatran, if you have collected 300 Pokémon in your Pokédex. On the left of the PokéCenter is a lab that allows you to battle Champion players who they have data on. After Saffron City is Route 21 and the next city which is Cinnabar Volcano.
Cinnabar Volcano, also known as Mt. Cinnabar, is where the seventh Gym is located. The Gym Leader's Name is Blaine and he specializes in -type Pokémon. There are a total of three houses, two of them of which are actually useful. The second one is for buying Pokémon and the third is for finding 'hunch' Pokémon in a specific route (Cresselia, Rayquaza, etc.). Some Pokémon you can find at Cinnabar Volcano are -type Pokémon and two Legendary Pokémon, Moltres and Regice.
Indigo Plateau is where the ninth and final 'Gym' is located. The Gym Leaders' names are Lorelei, Bruno, Agatha, Lance, and finally, Champion Gary. They specialize in -type, -type, -type, -type, and finally, a mix of Pokémon. This is also where you can access Elegant Valley, and obtain Giratina-O and Regigigas.
Victory Road is an area that has a lot of -type and -type Pokémon that are very high level, you can also catch the Pseudo-Legendary Pokémon Gible and Legendary Pokemon Dialga Registeel (you need to be Champion for Dialga).
Elegant Valley is where you can EV and IV train your Pokémon (click here for more information). You can also catch a Semi Pseudo-Legendary Pokémon, Larvesta, and a Legendary Pokémon, Palkia (you need to be Champion for Palkia).
Mysterious Grotto is where you can battle trainers in the Battle Tower. You can find different types of Pokémon in the vast wild Pokémon areas that can help you throughout your adventure and a Legendary Pokémon, Deoxys, can also be found at Mysterious Grotto and can change its form according to the meteorite you select. There is also a red entity in the back of the Battle Tower.
Mausoleum of Origins
The Mausoleum of Origins is a newly added area in Project: Pokémon that can only be accessed by players with 8 Gym badges. It has three houses, one of which is actually useful. There are newly added Pokémon from Generation V in new textured wild Pokémon areas that are stronger than Victory Road Pokémon and three Legendary Pokémon can be found here which is Meloetta, Zekrom, and Reshiram.
Snow Canyon is a Canyon next to Indigo Plateau where you can catch many of the Gen 6 Pokémon. There is a staircase which leads up a mountain to Red, who gives you a Mega Stone after defeated. There is also a ladder that leads to a cliff in which you have to bug your way through. there is another cliff, which you also have to bug your way through. There is another ladder that leads to nothing.
More areas to come in Project: Pokemon...