Raikou, Entei, and Suicune split as soon as you as you free them, and will spend the rest of the game wandering from Route to Route in Johto. You'll meet them again when you get into a random battle and one appears instead of a local Pokémon, but no one knows when or where.
Don't be afraid when you do encounter them: instead of attacking, these level 40 Pokémon will run away immediately (you may get to attack first, so use Sleep if your active Pokémon has it, but don't try changing Pokémon). Any damage you do won't heal, so after enough random encounters, they may be wounded enough to catch.
Actually, there is an art to tracking and capturing these cowardly but powerful beasts, which is discussed below. But first, you have to get lucky and run into each of them.
Changes in Crystal
In Crystal, you definitely haven't seen the last of Suicune: it will appear in several additional game events before you have a chance to catch it. Raikou and Entei, however, are in the wind now in all three versions. After you run into them once, you'll be able to track them with the Map option under their PokéDex entries.
After you get the Clear Bell from the Radio Tower, come back to Ecruteak's Pokémon Gold and Silver/Tin Tower to battle Suicune. One new twist in Crystal is that you'll need to catch Suicune, Entei, and Raikou before you'll get a chance to catch Ho-oh at the top of Tin Tower.
The Legendary Beasts
In Gold and Silver, Suicune has Leer, Water Gun, Roar, and Gust, and in Crystal it has Leer, Bubblebeam, Rain Dance, and Gust. The change is due to the fact that you can catch Suicune in Tin Tower in Crystal. Entei knows Leer, Ember, Roar, and Fire Spin and Raikou knows Leer, Roar, Thundershock, and Quick Attack. You get 1,234 EXP for defeating any of the Legendary Beasts.
To find them first you need to see them, then you can find which area they are in. A good place to check is Route 36, because of its links to other routes. If the Pokémon is to the left of Ecruteak City, then go into the link place between Ecruteak and Route 38. It is also good to check the Pokédex, because if you have seen a legendary beast, it will tell you where it currently is.
The easiest way to catch one is to make the Pokémon fall asleep, then swap to a Pokémon that can lower its health. Mean Look and others are good, but they can still use Roar to escape.
To catch a Legendary Beast, a few steps are needed:
- You must have three different types of Pokémon in your party.
- Your Pokémon must have Flash, Sleep Powder, False Swipe (or Tackle if you don't have Scyther), and 20-30 Ultra Balls.
Flash is used to reduce the accuracy of the enemy's attacks. It is also used to light up dark areas, like in Dark Cave. You can get this as an HM from the Head Monk at Sprout Tower in Violet City. Sleep Powder is used to make wild Pokémon sleep, and is preferred over other status ailments as, due to a coding error, sleep is the only status effect that increases catch rate, in addition to preventing the enemy Pokémon from doing anything. Tangela or Weepinbell are both Pokémon that have the move in their movesets. You can find both of these Pokémon on Route 44.
Scyther is a good Pokémon to use, because its False Swipe attack will take down enemy's health to 1HP, then miss every attack thereafter. You can find a Scyther in National Park. You can also use a low level Pokémon and the normal Tackle skill. Use level 20 to 25 Pokémon, because their Tackle skill will bring down the enemy's health from 1HP to 10HP per attack. You don't know how much HP the Legendary Beast has, so just get its HP down into the red. If you can leave just a little red on its health bar, it will be much easier to catch it.
You need Ultra Balls as well. you can buy them in Blackthorn City. You can get to Blackthorn City by following the Ice Path. It is recommended that you buy 20-30 balls before trying to catch a Legendary Beast.
Before you go into battle, make sure you line up your Pokémon party. The first Pokémon should know the Flash skill, like Magnemite or its second evolved form, Magneton. Use either Weepinbell or Tangela for your second Pokémon, either Scyther or any low level Pokémon with Tackle. Save your data at Tin Tower on your way to the fight.
During the fight, use Flash first to reduce the Legendary Beast's accuracy. Do this up to five turns until it says its accuracy won't drop any further. Then switch to your second Pokémon and put it to sleep. At this point, your goal is get the Beast's HP down into the red with your third Pokémon. If you get its HP down this low and it's asleep, it will be much easier to capture. Then start chucking Ultra Balls. They're your best bet, in lieu of using the Master Ball (which you SHOULD use on at least one of these Beasts, to save yourself at least one hassle).