Cipher Peon Resix (red) - Slugma 14, Hounder 17+
Cipher Peon Jirel (blue) - Horsea 11, Goldeen 12, Spheal 17+
Cipher Peon Browsix (orange) - Hoothoot 14, Baltoy 17+
Cipher Peon Yellosix (yellow) - Electrike 12, Chinchou 11, Mareep 17+
Cipher Peon Purpsix (purple) - Grimer 11, Koffing 10, Tentacool 10, Gulpin 17+
Cipher Peon Greesix (green) - Cacnea 9, Oddish 9, Shroomish 9, Lotad 9, Pineco 9, Seedot 17+

Beat and snag them all, and enter the lab. Explore around the corridors and lifts as in Colosseum, and will run into quite a lot of Cipher Peons with shadows:

Cipher Peon Maggie - Duskull 14, Skitty 14
Cipher Peon Rukiro - Doduo 13, Taillow 14
Researcher Eojin - Lileep 13, Anorith 13
Reseracher Shisto - Clamperl 13, Corphish14, Zubat 15
Cipher Peon Nexir - Shuppet 13, Swinub 14, Spinarak 14+

The researchers will speak of XD001 and Cipher being resuscitated again after being disbanded 5 years ago. Go further, and an animation will show the kidnapped Krane having a conversation with one of the Cipher’s Admins, Lovrina. Lovrina acknowledges Krane’s work in purifying shadows, and persuades him to help Cipher create a non-purificable shadow Pokémon. Krane declines, and Lovrina leaves to the kidnapper peon, Spy Naps, to reason with Krane.

Fight and snag more along the way:

Cipher Peon Solox - Ralts 15, Voltorb 16, Bagon 16, Numel 14+
Cipher Peon Kanta - Abra 17, Machop16, Feebas 16, Makuhita 16
Cipher Peon Lukig - Snorunt 14, Barboach 14
Reseracher Machin - Spoink 16, Lotad 14, Staryu 14
Cipher Peon Tibu - Natu 16, Nincada 14, Wailmer 15
Cipher Peon Cabol - Carvanha 15+, Magnemite 15, Psyduck 15, Remoraid 16
Researcher Enushi - Swablu 17, Wynaut 16, Corsola 15
Researcher Oodi - Dustox 14, Wingull 17, Pineco 16, Qwilfish 15
Cipher Peon Yagoru - Jigglypuff 15, Chimecho 17, Dunsparce 16

You will then enter a lab of two researchers who talk about XD001 being out of control. One of them will fight you:

Reseracher Heliko - Snubble 16, Kecleon 16, Shroomish 15+

Snag the shadow, and he will rush out to inform Lovrina. You pick up the elevator key on the table to access an elevator that was locked previously, and head up to the room where Krane is held hostage. Spy Naps fights you again:

Spy Naps - Murkrow 18, Rhyhorn 18, Slakoth 18, Beldum 18

Beat him and he will let you go, as he appears to disagree on the shadow Pokémon ethics anyway. Krane joins you, and you are about to leave when the researcher earlier brings Lovrina in to intervene. You fight the first Cipher Admin after refusing her offer to join Cipher:

Cipher Admin Lovrina - Luvdisc 20, Agehunt 19, Roselia 19, Delcatty 18+

Lovrina storms away after you beat her, and leaves behind a data rom on the floor. Pick it up and you will be back at the HQ lab.

Pokemon HQ Lab:
Krane tells you to have Buster try analyzing the data rom, and Jovi volunteers to do so. You mom, Lily, will speak of the Purify Chamber being completed, and you can start using it purify your shadows. You then head over to Buster’s room but Jovi says he went out after reading the rom. You go outside of the lab to find him, and he is upset because he fails to crack into the rom. Krane comes out to comfort him, and suggests you seek help from Nett in Pyrite Town, and off to Pyrite we go.

Pyrite Town:
Upon arrival, you see Duking’s daughter Leila who is now a journalist running out with a cameraman Puri chasing after her. This town is basically the same as before again, with the fortune telling lady Fateen is still there, and the sheriff is still sitting in his chair at the police station, with a chaser and a Snagem team member each locked up in one of the cells. Walk to the shop, and you will see an animation between the policeman and Miror B’s two underlings, Trudly and Folly. They are not welcome in town because of their acts 5 years ago, and the two men left with grudge.

Everyone in town seems to be talking about wild Pokémon, and you head to Duking’s house to find Silva being the one in charge of the Pyrite Stadium now. In the secret room at the back of his house, all the kids are gone and only an old woman is left behind who makes the Pokéfood PokéManma, to assist Duking in his search for wild Pokémon. There are several trainers in their old spots to fight:

Rogue Masa - Ralts 16, Snubble 16, Seedot 16, Hounder 16
Technician Habari - Spoink 16, Magnemite 16, Numel 16
Chaser Dia - Shuppet 16, Ledyba 16, Remoraid 16, Togepi 16
Hunter Rehbe - Zigzagoon 17, Whismur 17, Aipom 17, Dunsparce 17
Chaser Dugs - Swinub 17, Bagon 17, Murkrow17, Clamperl 17
Rider Orango - Slugma 16, Natu 16, Oddish 16
Bodybuilder Zebul - Machop 17, Tentacool 17

Arrive at the ONBS station to the right before crossing the bridge to the stadium, and Nett’s siter with her Shroomish will be the receptionist. Head up to find Secc, who is the technical director of ONBS, in his room is on the first floor. You will find a lost girl in one of the rooms on this floor also, and take her back to her mother on the second floor, who will reward you with the shell bell. Head up to the small room on the building top where Nett is, who is the manager of ONBS, and he will take the data rom from you. He tells you that the ONBS was originally called the Kids Grid and they existed to prevent the likes of Cipher from haunting Orre again, thus agreeing to spread news about Cipher’s possibly resuscitation.

Nett then informs you about Duking’s progress in searching for wild Pokémon, and wants you to go help him at the RockGround Pokéspot. Head there now.

RockGround Pokéspot:
Duking and a reporter lady Pufty will be here having an interview, and Duking will want you to try out how the Pokéspot works. He gives you the Pokéspot Monitor to your P*DA, and offers you 10 PokéManma to use. He also tells you of the two other Pokéspots he found, the Oasis and Cave, and wants you to head over to those places as well. Go to the Oasis Pokéspot.

Oasis Pokéspot:
Duking will appear again, and hopes you will find him the three rare Pokémon Wooper, Surskit and Trapinch. He then leaves and wishes you good luck. Head to the Cave Pokéspot now.

Cave Pokéspot:
Upon arrival, you will Folly and Trudly again, and a weird music plays, then Miror B arrives with a new outfit. Miror B is now a wanderer and is more like a mafia gang leader, in a weird sense of course. He will fight you:

Wander Miror B - Lombre 17, Lombre 17, Lombre 17, Voltorb 19+

Snag his shadow, and the three will run off. But they leave behind something on the floor, and you pick it up to find it as a Miror B Radar, which will let you know where Miror B is when it senses his location as you go along the game. Suddenly, you will receive an urgent mail from Secc telling you head back to ONBS quickly.

Pyrite Town:
Go to the ONBS station, and you will find it ambushed by Cipher. Fight the peons along the way to get to Nett’s room:

Cipher Peon Shian - Carvanha 18, Barboach 17
Cipher Peon Gyald - Corphish 18, Electrike 17, Grimer 18
Cipher Peon Torkin - Kecleon 19, Surskit 21, Makuhita 18+
Cipher Peon Mesin - Spinarak 20, Agehunt 19, Dustox 19, Vulpix 18+
Cipher Peon Rozard - Qwilfish 19, Rhyhorn 20, Chinchou 20, Koffing 20
Cipher Peon Randa - Duduo 20 , Tentacool 18, Chimecho 20
Cipher Peon Karti - Gulpin 19, Mareep 18, Luvdisc 20, Bellossom 21
Cipher Peon Eran - Furret 19, Zigzagoon 20, Togetic 19, Delibird 21
Cipher Peon Labor - Sneasel 20, Yanma 19, Misdreavus 20, Duskull 19+
Cipher Peon Forus - Flaaffy 22, Kadabra 22, Vigoroth 21, Ralts 20+

When you arrive at the room, a Cipher gang leader, Dakacha will threaten to kill Nett’s sister, and Nett had to exchange for her with the data rom. Fight him:

Cipher Cmdr Exol - Loudred 23, Giragarig 23, Mawile 22+, Raichu 23

Dakacha then says the database of ONBS has been deleted, thus removing all the data they’ve cracked into. He surrenders the data rom and says it won’t matter anymore, and confirms that the Libra incident is indeed the work of Cipher, and that Cipher is attacking Phenac. He then flees, and Nett urges you to warn Phenac’s mayor while they clear up their mess.