You read on the news that an evil organization is under investigation of the police force. You head outside the Pkmn Center and now a girl there will give you the cologne case to buy fragrance to massage your dark Pokemons. You head to the Unknown Lab.
You can't get in yet but upon arrival you receive another message from Ginzaru to tell you to go back to Pyrite. You head back there.
You head back to Ginzaru's place, talk to the kid in the secret room, and learn that they are in some sort of children network thing.
At the police station, Troy, Heboi, Reath and Ferma have been arrested. You get the jail key from the table, enter Reath and Ferma's cell, and get the elevator key from them. You go back to the Pyrite Building, find the Ein File titled R for revive somewhere, and use the elevator to head down to The Under City.
The Under City: (Shop, Children's Network Centre, JunkShop, Colosseum, Botomu Colosseum, UFO transport system)
Upon arrival, there's an animation on screen by Venus, the lady people are fascinated about, talking about a spy hiding in the city.
In this under city, you can fight some trainers on the street:
Sizu - Skitty, Jigglypuff, Oddish
Zakoru - Feebas, Magikarp, Wailmer, [Wailord]
You go into the JunkShop locared on the top right side of the main chunk of buildings, get downstairs to find a boy called Zakku. He knows the two of you from children's network and tells you to bring an enhance patch to Sureddo in his house. You leave the JunkShop and go to Sureddo's house on the far left of the city, which is also the Children's Network Centre. You give Sureddo the enhance patch and they ask for your P*DA number to communicate with you in the future. You leave the house to see that Siruba has come to spy on Venus and has been locked up by two Cipher battlers. You fight the two of them:
Cipher Peon - Kloak - Spinarak, Ledian (Dark 40), Volbeat
Cipher Peon - Igaro - Ariados, Gloom, Illumise
The two of them flee and you talk to Siruba through the gates. He gives you UFO disk R. You go to the UFO transport port, choose disk R, and the UFO will take you to a building on the right. You enter to find Venus interviewed by TV reporters again. But she spots you and fights you:
Cipher Admin - Venus - Steelix, Suicune (Dark 40), Delcatty, Banette, Vileplume
She flees underground and you give chase. You go underground further and see Venus escape in an elevator. You run down the spiral staircase and fight trainers along the way:
Frena - Shroomish, Gligar (Dark 43)
Liaks - Kirlia, Roselia, Gloom, Stantler (Dark 43)
Lonia - Octillery, Dunsparce, Masquerain, Piloswine (Dark 43)
Nelis - Seviper, Sneasel (Dark 43), Loudred, Corsola
You end up at the railway station where you enter to see Venus stole the key of the train Dark Liner. She runs away again, but she accidently drops the key in front of the station entrance. You see something sparkle on the floor and picks it up. You go back in, start the Dark Liner, which heads to the underground of the Dark Pokemon Lab. Some Cipher grunts blow up the underground entrance after you arrive and you can't get in. But you found on the floor the key to the main gate of the Lab and you also find the UFO disk U. You drive the train back to underground of The Under and head up.
At the UFO control port, use the disk U to go up to a secret room and get the second Flute of Time. Then use the disk F to go straight in front to enter the Colosseum. Take the elevator inside that building and it will lead you up to leave The Under without having to come in through Pyrite. Now The Under becomes accessible by your Spider Bike. Now go to the Unknown Lab now known as Dark Pokemon Lab.
This is how to get through af pyrre town.
All credit goes to serebii.net