Enter the Colosseum and talk to the lady. Answer "YES" to all of her questions. A Colosseum gauntlet follows with four rounds against the following trainers:
For winning the lady at the counter gives you $4,848 and the TM06 (Toxic).
The Cipher Hideout
Now it's time to enter the Cipher Hideout. Leave the Colosseum and go down the bridge. On the bridge you'll be confronted by a Cipher Peon. He won't battle you but he'll ask you to follow him. You're about to get awarded a Shadow Pokémon when the girl Peon realizes you're the guy who's been giving Miror B. all the trouble. Now the Cipher Peon will battle you.
Easy. Catching Yanma will be so-so difficulty, and Pineco, Surskit, and Nincada should all be killed in one hit.
Upon defeat, Duking and a few other people appear. You find out this is where Shadow Pokémon are being given to thugs for winning (if you didn't know that already), and that Duking's Plusle has been kidnapped. Now we've got to put a stop to Miror B.'s plans and rescue Plusle.
Leave the building and the city. Head back to Phenac for a very short detour.
Phenac City
Enter the Pre Gym in the middle of the second floor. Take a sharp left and talk to the lady at the whiteboard. She'll give you a P☆DA upgrade, a Strategy Memo, which is similar to a Pokédex. It gives data on all Pokémon met so far.
Head to Outskirt Stand. By now you should have few Great Balls, so buy as much as you can there. Now head back to Pyrite.
Pyrite Bldg
This section is incomplete. Please feel free to edit this section to add missing information and complete it. Reason: Moveset and abilities for all trainers, excluding those with Shadow Pokémon
Use a Pokémon that's good against Flying or just your needing-to-be-purified Shadow Pokémon.
You can now save and heal in the room right below the Roller Boy. Right below the healing machine is a well-hidden Ein File H. We'll learn more about the Ein Files later. Go up the stairs. You'll have no choice but to fight the next guy.
Just like Mirez from the Colosseum challenge, this is a challenging battle, although you'd think Larvitar, the basic form of a pseudo-legendary, would be harder. You can't go half a hallway until you find yet another two Trainers.
There's a Revive in the next room in the bottom-left corner behind the door before blue-haired Trainer who, surprise, surprise, will battle you without hesitation.
Apparently not now. You should go downstairs and heal/save anyway. Now you're on the roof when you get back up. Head left, ignoring the grunt, and enter the door. You'll find Silva defeated by two Miror B.Peons. Challenge time!
Mantine should present a challenge in catching, Furret's a beast, and Aipom and Yanma are so-so. After beating her, Silva will ask if you know Duking twice. Answer "YES" both times. Miror B. will show up on the television. He tells them he's been using Plusle as bait to get them to follow him. It's a perfect "tactic".
Ein File S is just there. Go downstairs and enter the elevator. Downstairs are 3 Hyper Potions. You're back in the lobby. Heal+save. Move your party around if you have to. Go back up the maze and you should now talk to the grunt. These guys just don't get it. You defeat their leaders yet they think they can beat you.
Goldeen and Linoone are so-so difficulty, Qwilfish can be pretty hard to catch. Remember you can catch Shadow Pokémon later at the very end of the game if you have to. He'll now finally let you into Pyrite Cave.
