Immediately when the game restarts, you get an email from Nett.
SubjectNew System Done! SenderNett from The Under
We, that's myself and Secc in Pyrite, developed a new system of downloading data automatically to your P★DA. From now on, information about Shadow Pokémon should arrive directly from people connected to the network. Check it out!
Go to Duking's house, behind the bookshelf. Talk to Secc, the little boy on the left side. He says Cail has seen a trainer with a Shadow Pokémon. Go talk to Cail to get some information, but he fights you first.
Go north until you come to an item chest containing a Max Elixir. Go right to find a PC.
Directly to the north of here is a narrow passageway. Every time you try to enter here, a Cipher Peon will drop down and battle you. They are trainers you've met before, so you can capture their Shadow Pokémon if you've missed them. The only one that's not optional is the first one, so battle him and go up the stairs. To battle the other ones, come back down the stairs and enter the narrow passageway and a trainer will battle. Repeat this process until you beat them all. Remember, the last five are completely optional.
As you go up the stairs, go right and through the nearby door to pick up the Elixir. The next few trainers are optional, and you have to go up to them and talk to them. Go down until you get to some stairs. Go up the stairs. Now go up and left. Battle the Team Snagem member if you want.
Just past him is a box containing two Max Revives. Go up the stairs now. You'll be in Gonzap's office. In the lower right hand corner is an item chest with three Rare Candies. Go back down the stairs.
Go up and up the stairs. Head south now, and go up these stairs. Now go all the way to the right and in the northeast corner of the floor, you can battle another trainer. He's not a Team Snagem member, but still, you can battle him.
To his immediate left is an item box containing three Max Potions. Go back to where the Snagem goon was and head down to that other item box that you picked up the PP Ups from. Take the nearby stairs. There's another item chest with two Max Ethers. There is also another trainer you can battle.
Head down. If you notice on the ground there are some Poké Balls on the ground. You can pick those up. Even though they look like Poké Balls, they're Ultra Balls. You'll get five of them. Continue ahead to your goal: the second Shadow JohtoStarter.