TL;DR (Quick Answer)
To visit Kanto in Pokémon Crystal for the first time, you must board the S.S. Aqua at Olivine City’s harbor and sail to Vermilion City in central Kanto. You can board the S.S. Aqua with the S.S. Ticket received from Prof. Elm at New Bark Town after you defeat the Elite Four and Champion Lance.
Note: You technically enter Kanto on your way to beat the Elite Four, but you don’t have access to any towns in the region at that time.
Afterward, there are a few different ways to cross the border between both regions. These include the S.S. Aqua and the Magnet Train.
To sail on the S.S. Aqua from Olivine City to Vermilion City for the first time, you need an S.S. Ticket. Here’s how to get it:
- Collect all eight Johto gym badges.
- Defeat the Elite Four and Champion Lance at the Indigo Plateau.
- Talk to Prof. Elm in his lab in New Bark Town to receive the S.S. Ticket.
Now, all you need to do is board the ship at Olivine Harbor.
Taking the S.S. Aqua to Vermilion City (First Time)
Make your way to Olivine Harbor. You’ll find the entrance southeast of the Pokémon Center in OIivine City.
Follow this path all the way down until you reach a pier.
A sailor from Fast Ship S.S. Aqua stands in the way. He’ll ask if you’ll be boarding today. Say “Yes” and show him the S.S. Ticket to leave for Kanto’s Vermilion City.
As you enter the ship, a well-dressed man bumps into you. After apologizing, he reveals that his granddaughter is missing.
We’ll have to help him find her to proceed.
Feel free to visit your cabin and heal your Pokémon by resting on the bed. There’s also a PC to change your party or retrieve items.
It’s the third cabin to the right, with a sailor standing by the door.
Once you’re done there, you want to head all the way to the right of the hallway and continue south as it turns. Then, use the stairwell leading to the lower deck.
A sailor blocks your path further into the ship.
He won’t let you through until you find his companion who’s ditching work and slacking off somewhere else.
The slacker sailor will be in the cabin next to yours on the upper deck.
Talk to him, and he’ll challenge you to a Pokémon battle.
His team comprises a Machop, a Machoke, and a Psyduck in the Lv.26-Lv.44 range. It shouldn’t be a problem after clearing the Elite Four.
The sailor will go back to his post after you win the battle. Now you should be able to explore the lower deck to look for the missing child.
Go past the sailor and to the left.
Continue down the hallway until it turns south, then head upstairs.
Enter the only door in this area. It leads to the captain’s quarters.
You’ll find the missing little girl here, asking the Captain to play with her.
Tell her that her grandpa is looking for her, and she’ll dart back to their cabin with you in tow. You’re automatically transported there.
The man will reward you with the Metal Coat for helping out.
The ship arrives at Vermilion City’s port immediately after receiving the Metal Coat. Just talk to the sailor near the exit to get off the boat.
Congratulations, you’re in central Kanto!
Crossing Between Regions (After First Time)
Regrettably, it’s impossible to use Fly to travel between regions. Instead you need to do one of the following to cross over:
- Sailing on the S.S. Aqua between Olivine City and Vermilion City.
- Surfing between New Bark Town and Route 27.
- Riding on the Magnet Train between Goldenrod City and Saffron City.
Let’s take a more detailed look at the options.
S.S. Aqua Between Olivine City & Vermilion City
After your first ride in the S.S. Aqua, it will continue to travel between Olivine City and Vermilion City twice a week, every week.
Its schedule is simple:
- Johto to Kanto: Mondays and Fridays
- Kanto to Johto: Wednesdays and Sundays
You can explore the ship and battle any willing trainers at your leisure.
To end the voyage and arrive at your destination, rest on your cabin bed. It will also heal your Pokémon!
Surfing Between Regions
Surfing between Johto and Kanto is the most reliable way to travel between regions before fixing the Magnet Train.
Do this whenever you need to cross over on a day the S.S. Aqua isn’t running.
Crossing from Johto into Kanto is easy. Just fly to New Bark Town and then use Surf in the water to the east. Keep going in that direction until you reach dry land.
From here, you can use Fly to reach any city you’ve already visited in Kanto.
Surfing from Kanto to Johto is a lot more complicated.
The closest place you can reach with Fly is the Indigo Plateau. You’ll have to run south through Victory Road and Route 26, then west through Route 27 to reach the crossing.
It’s the contrary of what you did on your way to face the Elite Four.
Once you’re on the western end of Route 27, just use Surf to swim westward into New Bark Town.
Magnet Train Between Goldenrod City & Saffron City
The most convenient way to travel between both regions is the Magnet Train, which runs between Goldenrod City in Johto and Saffron City in Kanto.
The Goldenrod Station is next to the Radio Tower. You can’t miss it.
You can find the Saffron Station in the northwestern corner of Saffron City. Just head northwest of the Pokémon Center and follow the road up.
Turn right when you can’t keep going up, and you’ll immediately see the station to the north.
Regrettably, the Magnet Train isn’t running when you first arrive at Goldenrod City, and it remains inactive when you reach Saffron City in the post-game.
To ride on the Magnet Train, you must:
- Repair the Kanto Power Plant east of Cerulean City by retrieving the Machine Part.
- Retrieve the lost Clefairy PokéDoll for the Copycat Girl in Saffron City to get the Magnet Train Pass.
With the trains running and your Magnet Train Pass in hand, you can finally travel on this high-speed railway.
Just speak to the clerk guarding the platform, and you’ll be on your way to the other region. It only takes a few seconds!