Walkthrough

October 14, 2022

This walkthrough was included with the Patch, replicated here for reference.

Goldenrod City

Go downstairs, and your mom, who is a nurse, will give you a Pokégear.
After this, go into Bill’s room in order to receive a Lv.5 Eevee (Your very first Pokémon, and your pre-starter) from him, who is your pal, in your home. He lives with your family now!
After that, you can explore the city a little, but many things are blocked by Team Rocket members. You must come back after you have helped Prof.Elm by giving him the Mystery Egg, and you receive your Pokédex.
You can earn a free Bicycle from the Bike Shop owner.
You can also receive a Lucky Egg in a house somewhere from an old man.
By talking to various people, you’ll learn how Team Rocket has owned the Radio Tower, ant learn how bad the closure of the World Terminal (including the GTS) has badly affected many people (Reference to HG/SS). You’ll also learn how bad casino games can be.
After all of this, just go to the teleporter in the basement of the Mart next to your home, which is the super Pokémon Center of this city. You’ll arrive in New Bark Town!

New Bark Town

Once you’ve teleported in New Bark Town, go see Prof. Elm at his lab to receive your second Pokémon starter (Lv 5 all): Houndour, Mankey or Natu! This will also mark the beginning of your trial to go to Mr.Pokémon’s house.
You can receive a gift of 5 potions from a man in a house, and learn a very important life lesson about shining.
You can also receive a TM03 from a woman, during the night only, after listening to her lesson about the importance of perseverance in life.
In the teleporter, you can also receive a gift of 5 Poké Balls by talking to the scientist.
Once you’ve done, go west to Route 29.

Route 29 and Route 46

Just go through Route 29 to reach Cherrygrove City. See for yourself how urbanism has spread onto the routes, not just in towns.
Some trainers are on the road, so be prepared!
You can go to Route 46 and talk to a man in a House to receive a Shuckle. However, note that the Shuckle is not really yours, since it does not have your ID Number. Also, it may disobey you, since it is level 15 and you don’t have a badge that grants obedience.

Cherrygrove City and Water Cave

Go into Tunnel 1, where the entrance is located in a house south of the Pokémon Center, and go to Water Cave to pick the item (a pearl) in there in order to access to Route 30. (That is a part of the trial!) Some trainers are on the way, so be prepared!
If you talk to the boy standing before the entrance of Tunnel 1, you’ll receive a Map Card for your PokéGear. He will go into the tunnel after this!
You can receive a TM47 (Steel Wing), the HM04 (Rock Smash) and the ItemFinder by going into the houses in these areas.
You’ll also learn what makes real friends if you visit a house.
After all of this, head north to Route 30!

Route 30

Fight the trainers on the way, who are part of your trial!
You can also buy some berries in the mart on this Route, if you’re interested. All kinds of berries are sold in there!
Head north to go to Mr. Pokémon’s house to receive a mystery egg and your Pokédex from Prof.Oak.
If you’ve got some Potions on you, speak to Mr.Pokémon in order to trade one for a Great Ball. This can be done repeatedly, as long as you wish and as long as you’ve got Potions on you. This is a great opportunity, coz Berry Juices are a better alternatives than Potions, and Great Balls are great, and you can obtain some for the price of a potion (300 dollars, which is half the price of a Great Ball), and you sell a Great Ball, it’s also 300 dollars, so it’s totally fair for you!
After that, return to New Bark Town. You’ll meet your rival on the way. He’s got 3 Pokémon, including the one he stole, so be prepared!
After that, head east to New Bark Town, and go into Elm’s lab! You’ll have to battle some Team Rocket members, and you’ll learn they have helped your rival to obtain (steal) a Pokémon from Elm. Once you’ve finished with them, and informed the name of your rival to one of them, they’ll leave.
After this, speak to Prof.Elm to deliver the egg to Prof. Elm. You’ve finished your trial!
After that, return to Goldenrod City via the teleporter.

Goldenrod City (Again!), Route 34 and Ilex Forest

Now, you can go the two special marts and the Name Rater in the north part of the city. Route 35 and 34 are also now accessible.
You can obtain a Coin Case in the special mart at north of the Train station. Once you’ve got some coins, you can trade them for great Pokémon as prizes, like Sneasel, Machop or Grimer, or items such as Moon Stones or Sacred Ash. Have a look for yourself!
Notice that all TMs and mails can be bought in this city from different clerks in the marts. Look for them all if you wish to have some!
You can also receive a Tyrogue from a man somewhere, but if you don’t really want it, you can trade it for a Heracross from a trainer somewhere in this city as well! Look for them if you wish!
Battle all the trainers on Route 34, and you can receive an Old Rod from the last girl trainer after you defeat her, before the gate to Ilex forest.
Go pick the Revive in Ilex Forest to gain access to the Gym. You can also receive a free TM02 (Swords Dance) from a boy next to the Revive.
After that, go challenge Whitney in her Gym to earn your first Gym Badge.
After you won the badge, go to the new flower shop (in a new house) to receive a Squirtbottle.
After that, head straight to the north on Route 36.

Routes 35, 36 and 37

Defeat all the trainers on Route 35 and National Park. (You could defeat those even before you can challenge Whitney if you needed training).
You can receive a Level 8 Farfetch’d from the guard in the gate to Route 35, but it won’t be yours, so you can’t rename it and may disobey you!
Once you are on Route 36, use the bottle on the tree, which a wild Sudowoodo at Level 18.
Notice the new lake on Route 36, but you can’t cross it for now. You’ll need to come much later, coz you’ll need Surf and Whirlpool to go to Violet City.
After that, go through Route 37, defeat some trainers and you’ll eventually arrive in Ecruteak City.

Ecruteak City, Tech Tower and Fire Cave

First, head in the Pokémon Center where you will meet your rival and will talk to you. Heal your Pokémon too! (Also, you’ll be able to trade with Gen 1 games from tomorrow, but it’s not mentioned in any way, coz it’s a secret…)
After that, go in the Dance Club to receive HM03 from the owner after you defeat the 5 Kimono Girls.
Somewhere in this city, in a canteen, there’s a scientist who can offer you an Ultra Ball in exchange for a Super Potion (If you’ve got some!). You can do this anytime you want, and as many times as you wish! It’s a fair trade to do, even though if you sell an Ultra Ball, you gain 600 dollars, and when you buy a Super Potion it’s 700 dollars, so you lose 100 dollars, but the fact you can obtain an Ultra Ball for the price of a Super Potion (instead of 1200 dollars), it’s a really fair trade for you!
There are some trainers living in this city who wants to trade some Pokémon. Look for them if you’re interested!
After that, go to the Tech Tower to pick a TM35 to the summit, which you must pick to access to the next step. You’ll also have to battle multiple trainers, including your rival (Also, there’s a shiny Mew (Level 9) hidden in this tower, if you’re interested to catch it! It ran away from a scientist…).
After you finish your walk in the Tech Tower, you can now go the Fire Cave via Tunnel 2 to pick an item in that cave (It’s a Fire Stone). It must be picked to gain access to the Gym. However, some trainers are waiting for you on the road, so be prepared!
After that, go in the Gym and win against Morty to earn your 2^nd Gym badge. You can now use Surf outside of battle.
After that, go east to Route 42 in order to surf and to go to Mahogany Town.

Mahogany Town and Lake of Rage

Go to the north at Lake Of Rage, defeat some trainers on the way and you’ll have to fight a Shiny Noctowl (Lv24). Of course, you can catch it, since it’s a rare sight. However, if you’re in the daytime, the Noctowl can be asleep at the start of the battle (strangely!).
After that, Prof. Oak will come to see you, and he’ll talk about Team Rocket’s milking business and wants to stop this. You’ve got to help him!
After that, go to Mahogany Town’s mart and defeat the Team Rocket members, as well as some wild Pokémon on the way controlled by Team Rocket on the B1F (Grimer, Porygon and Magnemite, at Level 22).
One you’re on the B2F, after an intense battle against a TR woman commander (Be warned, she has a Ho-oh on her team!), you’ve got to defeat or catch three captured Pokémon that were abused by Team Rocket (Tauros, Miltank and Flaaffy at Level 24 each!) You can catch those 3 Pokémon if you wish, especially Tauros and Miltank which are really rare in the wild!
After this, Prof. Oak will reward you with HM06 (Whirlpool), and he’ll leave in order to return to his lab in Pallet Town, saying that next time, he would like to have a Pokémon Battle with you! (For those who don’t know, Prof. Oak has regained his passion for battling while he was in Pasio (Source: Pokémon Masters)!)
Note: You’ll still be able to buy Moomoo Milk in the mart after this (It’s useful!). It’s just that now, it’s more controlled, and not really by Team Rocket…
After that, go to the Gym and defeat Pryce to earn your 3^rd Gym Badge, and gain the ability to use Whirlpool outside of battle.
After go back to Ecruteak City, in order to go south (Route 36) and surf to Violet City. You must have Whirlpool to surf there and clear the whirlpools on the way. After that, you’ll arrive in Violet City.

Violet City, Rock Area and Flash Tower

You can go to the school to learn about real friendship if you want.
Go to Rock Area (The access is at Route 31 at east) to pick the items there! Some trainers are on the way as well.
After that, go to the Underground Sector (North-east) to pick an item hidden down there, after you battle a TR Grunt.
Around 3-4 PM, you can see a woman in a house down there that will massage one of your Pokémon. You can also learn the importance of careers by talking to various people in that underground sector. You’ll find the Power Plant down there as well.
You’ve got to do the power plant’s quest, as the owner needs a machine part to upgrade his generator. Once you talk to him and exit the Power Plant, a phone call occurs, and you’ll be informed that an employee from the mart in this city has a great machine part. You’ve got to meet that employee.
Once you talk to the employee (scientist) in the mart of this city, go back deliver the machine part to the owner of the Power Plant. You’ll receive a TM07 (Thunder Wave) in return, and you gain the access to Route 32 (Useful for later!)
After that, exit the underground sector and go into the Flash Tower to receive HM05, which is Flash, from the leader of that tower! He’s quite strong, and lots of trainers awaits for you there as well. However, there‘s a doctor inside that tower who will heal your Pokémon, so don’t worry!
After that, go challenge the Gym and defeat Falkner to earn your 4^th Gym Badge.
After that, go pick a Pokémon Egg at the Pokémon Center as a gift from Prof. Elm from his young assistant. (You must have a room in your party to receive it!)
After that, head south to Route 32.

Route 32 and Union Cave

Battles all the trainers on this route and into Tunnel 4.
Once you reach the Pokémon Center, you will have a small evaluation from a girl if you know what is a real friend!
Heal your Pokémon, and you’ll see that upstairs is a Communication club. It works with a program named TGB DUAL.
After that, go into Union Cave and battles the trainers. You’ll need Surf!
Once you’ve got through the cave, head west to Azalea Town.

Azalea Town and Ilex Forest

Go to Kurt’s house and talk to Kurt to access to the Well. His cook will let you go inside the well.
Defeat Team Rocket at the Slowpoke Well.
After that, you’ll be sent to Kurt’s House by his cook, who congratulates you.
In Kurt’s house, the cook will regain his place (to the desk at east) and you can trade a WHT Apricorn for a Rare Candy he made himself anytime! This is a good chance for you!
After, you have to go in Ilex forest and talk to a ranger to gain access in the Gym (Everything is safe now!). You’ll battle your rival once more in the process.
After that, go to the Gym and defeat Bugsy to earn your 5^th Gym badge. You gain the ability to use CUT outside of battle!
After that, go to Ilex Forest and earn the HM01, which is Cut, from a ranger after defeating some trainers.
After that, use cut on one tree, and visit the shrine of the forest. You’ll encounter a Lv35 Shiny Celebi! This is a rare chance!
After that, go straight to the north at Ecruteak City, and cut the trees at west to go to Route 38.

Route 38, Route 39 and Ice Cave

Defeat the trainers on the road. However, once you arrive on Route 39, two men tell you that you need to go in Ice Cave before going south. You need to pick an item there.
Go to the Ice Cave by taking Tunnel 5 (From Route 39) and some more trainers are waiting for you. You can heal your Pokémon in a house on the road to the Ice Cave, so don’t worry!
Once you arrive near Ice Cave, you’ll meet a trainer named Adam, who is looking for great Pokémon challenges. You must challenge him if you want to go in the Ice Cave. He’s quite strong and he has a team of 6 Pokémon, so be prepared for a tough battle!
After this, Adam will leave, and go into the Ice Cave to pick the item (TM14) surrounding Raikou, Entei and Suicune (Who are frozen solid!). However, as you approach them, the ice on their body will melt, since they’ll sense your strong presence, and they’ll be free! You saved them!
After that, return to Route 39 and head straight to Olivine City at south.

Olivine City and Light Tower

Go in the underground sector (Entry at north-east) and pick the item down there. Some trainers are inside, so be prepared.
You can also visit the second floor of the Pokémon Center to meet three Nugget traders, where you can trade a Nugget for a batch of great items. One will exchange you 12 Ultra Balls, another one for 10 Revives and the other one for 5 Full Restores, each for only one Nugget in return at a time. These are great deals for you, if you’ve got some Nuggets on you.
After that, go in the Light Tower and rescue Jasmine from Team Rocket. However, you’ll meet your rival once again, and many trainers are waiting for you too, so be prepared for tough battles, especially against your rival and Team Rocket’s commander Alexandre. You’ll also learn something important concerning your rival during your quest in that tower.
Once you arrived to rescue Jasmine at the summit of Light Tower, she’ll think that you’re from Team Rocket, and so, she’ll battle you, but it’s not an official GYM battle, so you won’t earn her badge. After you won, she’ll realize her mistake and she’ll be sorry. However, since you defeated her Ampharos, Jasmine will ask you to bring her a great potion, from Cianwood City’s mart, in order to repair your own mistake of defeating it. (Et oui!)
After that, exit the Light Tower and go west to Route 40, and prepare yourself for a long SURF ride! Have some repels, which you can buy at the local mart!

Route 40 and Route 41

Surf on the sea and battle all the trainers on the way.
Be prepared for a long surf ride in a big sea maze on Route 41! Have lots of repels!
You’ll eventually reach Cianwood City!

Cianwood City

You can go in the Mart to receive a free TM46 (Thief). You’ll be informed that Team Rocket, who has invaded the Safari Zone, has stole the last Secret Potion as well. You’ll need to get it back later, precisely after you get your 6^th Gym Badge from Chuck, since a man prevents you from going to Route 47 and beyond.
You can go battle Ash Ketchum at the Trainer Club in this city. You’ll also learn something quite interesting: How does aging works on Pokémon World. (It’s really not the same as on Earth!) They’re two separate planets, and so, two different worlds!
After that, go challenge Chuck and his Gym and defeat him to earn your 6^th Gym badge!
After that, you can speak to a sailor in the city to receive a TM17 (Encore). He’ll encourage you to go defeat Team Rocket at north.
After that, you’re now allowed to go to Route 47. Head north to enter in the mountain tunnel that leads there!

Route 47, Route 48 and Safari Zone

Defeat the trainers on the way, including Team Rocket members and your Rival as well.
Go to the north and head straight to the Safari Zone’s area. However, Team Rocket owns the place now.
Once you arrive in the Safari Zone, you can heal your Pokémon by talking to a doctor in a house, so don’t worry!
After that, go inside the Safari Zone itself (divided in 3 huge wild areas), and look for two Team Rocket men inside, who are really strong! You have to defeat them, and once done, one will give you the HM02 (Fly), and the other will give you the SecretPotion, which you need to heal Jasmine’s Ampharos that you have weakened before by mistake.
After this, many TR members leave the area, but some will stay to guard the area (It’s still their property, coz they bought if from Baoba, who sold it to them in fear of them!).
You can catch some rare Pokémon inside if you wish. Some of them only appear there, so enjoy it! However, since it’s the property of Team Rocket now, the ambiance is so much sadder (the music really expresses it!)…
After that, fly back to Olivine City (With Fly is much better!).

Olivine City (Again!)

Head back to the Light Tower and give the secret potion to Jasmine. She will heal her Ampharos, and leave after to return to her Gym.
After that, go fight Jasmine at the Gym and win your 7^th Gym badge.
After that, Prof.Elm will call you, informing that Team Rocket has modified the local Radio programs. So, you must head to Team Rocket’s Radio Tower, in Goldenrod City, to face Team Rocket once more!

Team Rocket’s Radio Tower (Goldenrod City)

Defeat the Team Rocket members, until you reach 3F to battle Alexandre, the TR member who has modified the radio programs. You’ll have lots of rematches with previous members you encountered before! (Hé hé!) However, some TR members are really strong as well, so be prepared for tough battles!
After that, go to the 5F in this tower to defeat Blaine to earn your 8^th Gym badge! (Yes, Blaine is the boss of this tower now, because he was homeless before, and he succeeded to become a “boss” for Team Rocket. In fact, he wanted more to have a new Gym, and so, this tower is kind of his new Gym for the time being…)
After all of that, fly back to Mahogany Town, and you can finally go to Route 44.

Route 44 and Ice Path

Defeat the trainers on the way and go to the Ice Path.
Some trainers are waiting for you inside the Ice Path as well.
You’ll eventually reach Blackthorn City after your travel in the Ice Path.

Blackthorn City and Dark Tower

First, go fight Clair in her Gym and win against her.
After that, go to the Dragon’s Den and pick the Dragon Fang there. You will receive your 9^th Gym badge from Clair.
After that, go into the Dark Tower and pick the item (TM03 Curse) at the summit. You’ll fight many trainers with dark thoughts and your rival inside this tower, so be prepared for tough battles! Don’t worry, a doctor is inside that tower, but he’s quite far, so bring some sacred ashes, revives and potions if you wish to succeed…
Once you have got all the items from Dark Tower, you gain access to Routes 45 and 46.

Routes 45 and 46

Defeat the trainers on these routes. Be prepared for some tough battles on the way!
Notice: You must go on the new Mountain Bike Cycling Road in order to reach Route 46 (at south) to pick the items there. You should have got the Bicycle already very early in your quest (If not, it’s in Goldenrod City).
After you pick the items on Route 46, return to Blackthorn City and go to the 2F of the Pokémon Center there to go into a teleporter that will teleport you to Route 27! You’re in Kanto now!

Route 27, Route 26 and Mt. Silver

Defeat all the trainers on the way and head north to the big gate on Route 26.
In this area (From Route 26 to Mt. Silver included), you can meet some people (Mainly in houses) who are Apricorn collectors. If you got some star pieces, big pearls or big mushrooms, you can trade them to get apricorns from them, except the white apricorn (For a Star Piece, you could get a red or a black For a big pearl, you could get a blue, yellow or a pink one. For a big mushroom, you could get a green one). While you may think it’s a worthless trade coz of their price value, apricorns will be useful for you later in your quest… They’re not just used to make Kurt balls, you know! Also, you can’t buy apricorns at marts, so…
Once you’re in the big gate on Route 26, you’ll need to have at least the8 badges of Johto to pass. Normally, you already have those, and one more badge from Blaine in the Radio Tower, so you shouldn’t have problems at all!
After that, you have the choice to go on Route 28 and Mt. Silver at west for some training, or to go east to Route 22. N.B. (The Victory Road (and so the League) is blocked until you have all the 16 badges and you have talked with Prof.Oak.)
If you go at west, so on Mt. Silver, you’ll meet some trainers and some rare Pokémon living there, including a shiny Tyranitar at Level 58. Also, two of the apricorns collectors are there as well. However, the cave has collapsed, and so, it’s now totally blocked and impossible to go inside.
To progress in your quest, you have to go east on Route 22, in order to reach Viridian City.

Viridian City

Since there’s no more Gym in that city, there’s almost nothing to do in this city, except to heal your Pokémon at the Pokémon Center and to buy some items at the Mart.
You can go to the new lab in this city, which is a huge building with 3 doors, to receive a Lv34 Chansey (which knows Softboiled and is nicknamed Nursey) from a retreated Nurse Joy, and you can also trade a Pearl for an Ether from a scientist (who makes Ethers) there as well. This trade can be done repeatedly as long as you have some pearls on you.
Also, you can have another evaluation on real friendships from a boy in the city.
You can also receive a free TM27 (Double-Edge) from a lady in the city.
You’ll also meet your rival once again in the Pokémon Center, and you must talk to him in order to gain access to Route 2. He’ll inform you that he’s looking for a new path in his life, and he’ll leave after.
After that, head north to Route2, coz you’ll need to find an item in Fuchsia City to go south (Which is far later in your quest).

Route 2 and Viridian Forest

Just go north and defeat the trainers on the way. Get ready to have some tough battles as well!
Have some repels on you when you’re into the forest, coz wild Pokémon are everywhere in the forest, like in a cave.
Eventually, you’ll reach Pewter City.

Pewter City (Including Valor Tower)

Go into the museum and defeat Brock on the second floor to earn your 10^th Gym Badge. You can always come battle him later if you’re not strong enough, coz you can still go to Cerulean City, and the areas at north to have some more training if you need too. However, he must be defeated before challenging Misty!
You can also train in the new Valor Tower in this city, which is the tower of Team Valor (Ref: Pokémon GO). There’s also a wild Moltres at Level 60 at the summit as well, but you can meet it only if you defeat the 3 trainers inside the tower. However, it can flee the battle (by escaping through an opened window in the tower), so be prepared for a hard catch, unless you have a Master Ball…
While you’re in the museum, you can learn some good facts about technology written on the computers, and also, if you got some Stardust, you can trade one for a Moon Stone by talking to a man inside, which can be done repeatedly. If you don’t have any Stardust, you can always buy some at the Mart for 2000 pokedollars each. There are also Star pieces on sale, if you’re interested to get apricorns from people on Mt.Silver and Route 27…
After that, go to the 2F of the Pokémon Center and teleport yourself at Cerulean City.

Cerulean City (Including Cerulean Cave)

If you defeated Brock, go to the new harbor, and you’ll bump into a member of Team Rocket that will run away.
Defeat Misty at this new harbor in order to earn your 11^t^h Gym badge. She’s really strong, like other Kanto Gyms, and as I said before, if you haven’t defeated Brock, you can’t have access to Misty’s place.
You can also visit the Cerulean Cave, and at the end, you can battle and catch a shiny Mewtwo at Level 65. It could be useful, and it’s the only one in the game too. However, it’s optional!
You can also trade a big pearl for a Big Mushroom from a man in the city. Since you can’t buy big mushrooms anywhere, and you can buy big pearls at the local mart, it’s a good trade to do, and it can be done repeatedly. However, the price may be quite high…
Once you’ve defeated Misty, you need to find an item north of Route 25 to progress further, or in other words, to gain access to Route 9.

Routes 24, 25 and Legend Island

Just go north, and then at east, and defeat all the trainers on the way, including some Team Rocket members.
Once you’re near Tunnel 6’s entrance, defeat Maxis, a member of Team Rocket you met before in Johto, who is blocking the access to Legend Island. Once defeated, he’ll leave with his crew.
After that, go into Tunnel 6 to reach Legend Island. You have to choose the correct teleporter to go through each room.
Once you’re on Legend Island, go pick the item (a TM39 (Safeguard)) in the center cave of the island’s cave. However, you must fight one more trainer before picking it.
If you’ve got the Rainbow and Silver Wings on you, you can catch a Lv55 Lugia in the basement of the cave, and a Lv55 Ho-oh at the summit of the cave.
After that, head back to Cerulean City and you now have access to Route 9 (at east). Prepare yourself to go there for the next step of your quest.

Route 9 and 10 (Including Instinct Tower)

Just go east to reach Route 10’s Pokémon Center, and defeat the trainers on the way.
You also train in the Instinct Tower on this route, which is the tower of Team Instinct (Ref: Pokémon GO). There’s also a Lv60 Zapdos at the summit of this tower as well if you’re interested to catch it.
You can also visit the Power Plant at south of the Pokémon Center on Route 10, and you can even get a Lv58 Magneton, nicknamed Magnus, from a retrograded employee inside.
Once you’re inside the Pokémon Center on Route 10, go on the second floor to go into the teleporter that will teleport you on the 2F of Lavender Town’s Pokémon Center.

Lavender Town

Once you quit the Pokémon Center, two Rocket trainers you met before will challenge you in a battle. Be prepared!
There’s nothing to do in Lavender Town, but you can buy some good things at the Mart, like Sacred Ashes.
Notice how sad this town is now… and some Team Rocket members patrol here as well…
After that, head south to Route 12, since Routes 8 and 10 are no longer accessible due to the mountains’ rising.

Routes 12 and 11

Defeat some trainers and just go until half of this route, coz a fisherman and Maxis (Team Rocket) are having a heated and long discussion. You’ll need to find an item in Celadon City to gain access to the south and to progress further.
So, head west to Route 11 and defeat some more trainers on the way.
Once near the end of the route, you’ll see a big wild Snorlax sleeping quietly. You have to tickle it in order to wake it up and to fight/catch it if you’re interested. It’s Level 65, so be prepared!
After that, you’ll eventually arrive in Vermilion City.

Vermilion City (Including Tower of Speed)

You can go to the Fan club to receive a Magnet Train pass from a woman there. You can also learn some good things about real friendship.
You can also train your Pokémon in the new Tower of Speed. If you win against the 3 trainers, you’ll receive 2 Pink apricorns, which you can exchange for 2 Carbos at the Apricorn Lab in Celadon City.
After that, you can go fight Lt.Surge at his restaurant Gym to earn your 12^th Gym badge. However, you can always come later, since he’s really strong!
Go north to Route 6 after that to reach Saffron City.

Saffron City (Including Tower of Defense)

Notice: Routes 5 and 8 are no longer accessible!
You can train your Pokémon in the new Tower of Defense. If you win against the 3 trainers, you’ll receive 1 green apricorn and 1 yellow apricorn, which you can exchange for Iron/HP UP respectively at the Apricorn Lab in Celadon City.
You can challenge Sabrina at her Gym in order to earn your 13^th Gym badge, which serves also as a place where the electricity of this city is controlled. However, you can always come later, since she’s really strong!
If you need to go back in Johto, you can always take the Magnet Train if you’ve got the Pass in Vermilion’s Fan Club from a woman there.
After that, go west to Celadon City.

Celadon City (Including Tower of Offense)

There’s no more Gym anymore in this city, since Erika has moved to Fuchsia City to join Janine. Plus, there’s no mart and no Game Corner anymore.
Also, Route 16 is no longer accessible due to an overgrowth of trees! Wild Pokémon now live in this city, in a patch of grass at west.
You can train your Pokémon in the new Tower of Offense. If you win against the 3 trainers, you’ll receive 1 red apricorn and 1 blue apricorn, which you can exchange for Protein/Calcium respectively at the Apricorn Lab in this city.
As I said before, you can visit the new Apricorn Lab in this city to exchange your apricorns (except the white apricorn) for various great medicine items, including PP UP. If you thought apricorns were useless before, think about it twice, you might change idea!
Go in a house south to pick an item on a table were two elderly people live. It’s a Moon Stone for you! The elderly man will then inform, via cellphone, his friend on Route 12, who is the fisherman that was blocking you, to go away in order to let you pass!
After that, head back to Route 12, which is east of Vermilion City. You now have access to the south part of Route 12!

Route 12 (Again!), 13 to 15

Just head south and defeat all the trainers on the way. However, some are scary strong, especially the Pokéfans who use Berserk genes, and one use a defensive Team with leftovers. Be prepared for serious battles!
Remember that if you have lots of badges already, these will help you a lot, as they make all your Pokémon stronger, even if you’re at levels lower than your opponents!
Eventually, you’ll reach Fuchsia City.

Fuchsia City (Including Mystic Tower and 2 new islands)

Go in Baoba’s house at the north in this city to pick an item, which is a Master Ball. You’ll also learn why Baoba left the Safari Zone in Johto… You’ll gain access to Route 1 from Viridian City now!
After that, go defeat the 2 gyms in this city, or in other words, Janine and Erika. Get their respective Gym badge, and you’ll have your 14^th and 15^th Gym badges. You can choose the order you prefer, or you can come back later if you wish!
You also train in the Mystic Tower in this city, which is the tower of Team Mystic (Ref: Pokémon GO). There’s also a Lv60 Articuno at the summit of this tower as well if you’re interested to catch it.
You can also go into the teleporter on the 2F of this city’s Pokémon Center to visit two newly discovered islands at south of Kanto (Simply named New Island 1 and New Island 2). You can get some great items out there, as well as some battles with trainers and some other surprises. Just relax and visit these new islands!
After you’ve done your visiting, fly back to Viridian City in order to go to Route 1, and so, to Pallet Town.

Pallet Town

After traveling through Route 1, you’ll arrive in Pallet Town.
You can try to challenge Red in his big manor. He waits for you at the 4F. You can meet his family and friends, and even your rival, inside. However, before battling Red, a sage (Red’s protector) wants to battle you in order to verify if you’re strong enough to face Red. Red uses a Sun Team, so be prepared. Once defeated, Red will quit his manor to go to the Pokémon League… (He won’t tell you this, however!)
You can also heal your Pokémon inside Red’s Manor from his nurse, if you need to.
You can also meet Prof. Oak at his lab and talk with him. At first, you’ll need to have a battle with him and his Lv90 Mew. Once beaten, he’ll evaluate your Pokédex and verify your number of badges.
After that, surf south, on Sea Route 21, in order to reach Cinnabar Island.

Cinnabar Island

First, talk to Blue, who stands in front of the Pokémon Center. He will then go to the 2F of this Pokémon Center. Heal your Pokémon after that.
After that, go to the 2F of the Pokémon Center and battle Blue in order to earn your 16^th Gym badge, and the final one! He’s really strong, by far, and he uses a powerful Rain team, so be prepared for a really tough battle!

Pokémon League (Indigo Plateau) and after!

If you don’t have all the Gym badges, well, return to the cities that you decided to pass them. Try to remember them, and fly to these towns. (The Kanto badges aren’t displayed in your case, which is sad…)
If you’ve got all the 16 Gym badges, you have to go to Prof. Oak’s lab and talk with him. He will let you access to the Victory Road, and so, to go to the Pokémon League (Indigo Plateau).
Once you’re arrived at the Pokémon League, you can battle Red and other trainers (including me!) in the basement. You can also face your rival on Mondays and Wednesday at the League too! Of course, you can also begin your Pokémon League challenge VS the Elite Four and Lance!
Once you’ve won the league, Prof. Elm would like to talk to you in order to congratulate you for beating the league… and he will reward you with a great prize of 2 Master Balls! Congratulations!
Finally, this is the end of your quest! I hope that you’ve enjoyed it a lot! You can now do what you want in these futuristic Johto and Kanto regions.
You can always retry the Pokémon League, rechallenge the 6 training towers in Kanto, and rechallenge Red as well. A note about Red: Once you beat Red in his manor, he goes to the League, and you beat him there, he returns to his manor. It’s always this way!
There are also possible rematches against some trainers via the PokéGear, and on their 3^rd time, their Pokémon are around Level 90-99, so it’s good challenges for you!