Finding Johto Starter 2
You start in the Outskirt Sands. You'll get an e-mail. Head to the Under and talk to Nett. Go to Pyrite Town and talk to a kid behind the bookcase. It says that Cail fought a Pokémon Trainer with a Shadow Pokémon. Talk to Cail who will battle you. If you didn't snag his Furret he'll have it. After you battle him, he says it's in the Snagem Hideout, which is now on the map. Head there.
Up to six Pokémon Trainers with Shadow Pokémon that you failed to capture will appear. They won't let you by until you've snagged all their Pokémon. This includes Skrub with Hitmontop and many other minor Peons.
Why are you here? You're looking for one of the other Shadow Pokémon starters.
All Trainers here don't have Shadow Pokémon and are optional. Search the base until you find him. He's below a Snag Machine.
Cipher Peon Verde/Rosso/Bluno
Level 53 Sharpedo (Verde only)
Level 53 Breloom (Rosso only)
Level 53 Camerupt (Bluno only)
Level 54 Grumpig
Level 51 Muk
Level 30 Shadow Bayleef (Verde only)
Level 30 Shadow Quilava (Rosso only)
Level 30 Shadow Croconaw (Bluno only)
Snag the starter he has and leave the base. Next up is the last one.
Finding Johto Starter 3
Finding Smeargle and Ursaring
Gonzap and Deep Colosseum
Rematching Realgam Tower Trainers
Simply head back to where they were in Realgam Tower. You can reface all six Trainers atop it as well, including Nascour and Evice. You can't rematch the three Cipher Peons who had Shadow Pokémon in the first part of the Tower with the rails.
The Final Shadow Pokémon
Once you have seemingly every Pokémon you'll start getting tons of e-mails. It'll lead you to the Outskirt Sands, where one last Trainer is...
Shady Guy [your name]
Upon defeating him, he'll reveal he's the Cipher Peon Fein, master of disguises. You should now try to purify every last Shadow Pokémon and complete the game entirely.