After the battle, Duking will come in and reveal to you that his Plusle has been taken hostage by Cipher and you need to get it back. Grab the binder, which is Ein File H, which gives you information on Hyper Mode.
The whole building is a giant maze to the top. There are a lot of trainers in this building, which means lots of EXP and money. Also, it is beneficial for your Shadow Pokémon to become more purified. The first trainer is guarding the elevator.
You should probably go back down and save and heal. Go all the way up and you'll be on the roof. Enter the little penthouse and you'll see another cutscene with Reath, Ferma, and Silva. Reath and Ferma attack Silva. Apparently Silva is always in the wrong place at the wrong time. After some conversation, you will fight both trainers.
To the right of the Hunter is a box containing a Full Heal. Now go back to the fork and head right, and up the stairs. You'll now be in a sewer system, or something of the like. Head left and you'll be in another battle.
After beating her, continue left and you'll find a PC and a healing station! Save your game, edit your team, and do whatever you need to do, then head up the stairs. You'll find two more optional battles in this part of the cave by going east.
After you beat him, he runs away, all four Ludicolo after him. After this, you hear a cry, which Rui identifies as Plusle's. Open the nearby box to receive TM49 (Snatch), then head into the back room. Pick up the Macho Brace, as well as Ein File P, a report on Purification.
Talk to Plusle, and Duking and Silva will meet up with you. This will trigger a cutscene that will bring you back to Duking's office.
After some dialogue with Duking, Plusle decides it wants to join us, so Duking lets us have it.
As we try to leave Pyrite Town, now that Miror B. is gone, you will notice Fateen the fortuneteller standing outside her house. Talk to her and it triggers a cutscene in which Rui remembers she was on her way to see her grandparents in Agate Village before she was captured. Now our next step in our journey is to see them and get some more information about purifying our Pokémon.