When you get to Mt. Battle and battle to the top, you will face Cipher Admin Dokim. He has Entei as a Shadow Pokemon.
To get Ho-Oh, purify all 48 Shadow Pokemon and defeat 100 trainers on Mt. Battle using only the Pokemon from your story mode team. Note: Your PC must have an empty slot.
Purify all 48 Shadow Pokemon; complete Mt. Battle in story mode; and complete Mt. Battle in battle mode. After doing all of this, you should be rewarded with Ho-oh.
Raikou can be found as a Shadow Pokemon of Cipher Admin Ean in the Shadow Pokemon Lab.
Defeat the Deep King Agnol in the Deep Colosseum. If you have all the Shadow Pokemon you will get a message about someone attacking people with a Shadow Togetic. Rush to the Outskirt Stand and fight him.
Croconaw, Bayleff and Quilava
After getting one starter Shadow Pokemon at the beginning, you need to get the rest of them. Complete the game and go to the Snagem Hideout. Look through the hideout until you see a man in only one color (green, blue or red). Battle him and snag his Shadow Pokemon. You will soon get an email. When you get it, go to the Kids Guild and talk to Nett. Then, go by the Junk Shop and fight Gurks. Talk to Gurks then go to the Shadow Pokemon Lab. Go to the last room of the Lab (where you fought Ein). You will see a person. Battle him and snag his Shadow Pokemon.
The second time that you battle Folly and the other person you will encounter three people in either Green, Red or Blue at all the entrances or exits. Battle them but do not defeat them. Just snag and lose and just attack yourself. You will snag all Croconaw, Bayleaf and Quilava, and on your third battle snag and win.
Catching the Legendary dogs
All three Legendary dogs (Entei, Suicune, and Raikou) are best caught with Ultra Balls, but it possible to do it with Great Balls.
When the Legendary Pokemon are on red, use a Pokeball. If it does not catch the Pokemon, use a Great Ball and it will be as if you used a Master Ball.
Getting the three starters
You can get the remaining starters after you complete the game. You will receive an email that tells you where to go. You will then get another email that reveals the location of your last starter.
Successfully complete the game, then go to the Deep Colosseum. You will find Silver Teeth as you are about to enter. Go to the old man outside the herb shop. Give them to him, he will give you UFO Disk -L. This will enable you to go left and get the Amulet Coin. The Amulet Coin gives you more money when you use the Pokemon equipped with it in battle.
A girl east of the Pokemon Center in Agate Village will give it to you. She is in blue clothes. Answer "No" to her in order to get it.
The Cologne Case is found in Agate Village. A girl with a blue shirt gives it to you. Go to the Deep Colosseum after you get the Amulet Coin. Give the Amulet Coin to Umbreon or Espeon. Win the challenge and you will get about 44,000 coins. Then, go back to Agate Village and to the Pokemart. Buy Vivid Scents and give them to your Shadow Pokemon to purify them.
F-Disk: Defeat Dakim at Mt. Battle.
R-Disk: From the kid locked up in the cage, in the Under.
U-Disk: In a chest, in the Subway, near the boxes.
D-Disk: Defeat Head Gonzap in the Snagem Hideout.
L-Disk: Talk to the old man in front of the Herb Shop.
Go behind Eagun's house and down the slope. You will find a chest containing an Exp. Share.
Use the D-Disk on the UFO. Keep hugging the left wall while pressing [A] and you should get the Steel Teeth. Talk to old man in front of the herb shop. Give him the teeth and he will give you the L-Disk.
As you enter Agate Village, turn right after the hill and go across the bridge. Directly in front of the "P.C." sign is a hill leading down. Go down this hill, then move downward. Follow the path to the right around the side of the hill and open the little box to find the Quick Claw. The Quick Claw is a hold item that often lets the Pokemon holding it attack first in battle.
The first Time Flute is obtained after you defeat Dakim. The second Time Flute is obtained when you put the U-Disk in the UFO (it is in a chest in the room).
A third Time Flute can be found on the 100th Mt. Battle area. In order to get it, you must have at least level 60 Pokemon.
To get the Train Key, go down to the train station. Go in and Venus will be there. Follow her into the train. However, she will not be in there. Go back out and Venus will be there. She will talk to you, then leave. When you go out of the train station, you should she something shiny on the ground. Go over to it and pick it up. It will be the Train Key. Go back to the train and use it. It will take you to where you need to go next.
Deep King Agnol
Complete the Deep Colosseum four times. On the fifth time you should fight Deep King Agnol in the last match.
Use the F-Disk on the UFO. Instead of going in the Under Colosseum go left and up to find a Herb Shop.