Pokémon Colosseum

Outside-City Stand:
After that, you're back at the stand where you'll receive a mail from the children's network telling you they've recovered more data from the DataRom stolen from the lab. You receive another mail telling you to go back to Masa in Pyrite Town. You beat him and he'll tell you about spotting a trainer with a dark Bayleef (actually, this depends on which you choose at the beginning, I chose Quilava). Then you'll be able to go back to the Team Snagem building you blew up at the beginning of the game. Go there.

Team Snagem Hideout:
Inside, you'll beat a consecutive number of Cipher members and other trainers:

Cipher Peon - Nore - Forretress, Ninjask, Agehunt, Masquerain
Snagem - Bagusa - Vigoroth, Rhyhorn, Grovyle, Zangoose
Cipher Peon - Skrub - Huntail, Wobbuffet, Medicharm, Golem
Cipher Peon - Coruga - Volbeat, Illumise, Ariados
Cipher Peon - Jinni - Vileplume, Roselia, Jumpluff
Cipher Peon - Arton - Sealeo, Piloswine, Glalie
Cipher Peon - Dioge - Masquerain, Forretress, Dustox
Snagem - Beiru - Pelipper, Lanturn, Seadra, Starmie
Mendo - Shellgon, Pupitar, Carvhana, Spinda
Rikaru - Linoone, Poochyena, Grayena, Kadabra
Chento - Linoone, Sandslash, Weezing, Swalot
Snagem - Digitas - Beautifly, Delibird, Swellow, Golbat

Then, you'll find the Greenranger
Mystery Troop - Verde - Muk, Bayleef (Dark 30), Sharpedo, Grumpig

Next, you move to any other region and you'll receive mail telling you to see Zakoru in the JunkShop at The Under. Beat him and he'll tell you about dark Crocronaw (again, depends on your choice). You receive another mail about going to the destroyed lab. You head there.

Dark Pokemon Lab:
You have to beat some Cipher battlers again first before finding the Blueranger at the main control room:

Cipher Peon - Lare - Hounder, Sneasel, Sharpedo, Nuzleaf
Cipher Peon - Vana - Golbat, Swablu, Mawile, Pupitar
Cipher Peon - Kabechi - Masquerain, Rhyhorn, Grovyle
Cipher Peon - Tanie - Delcatty, Linoone, Vigoroth
Cipher Peon - Remil - Swellow, Kadabra, Quagsire, Kecleon
Mystery Troop - Bluno - Crocronaw (Dark 30), Grumpig, Muk, Camerupt

Move to another place and you receive mail again about some Team Snagem members back at their hideout. You go back to the destroyed hideout again.

Team Snagem Hideout:
Fight some trainers:

Uis - Flaaffy, Dunsparce, Octillery, Walrein
Nelis - Sharpedo, Corsola, Seviper, Loudred
Liaks - Noctowl, Gloom, Golduck, Jumpluff
Heshity - Jigglypuff, Shroomish, Mawile, Donphan
Snagem - Biden - Smeargle, Smeargle, Smeargle, Smeargle (Dark 45)
Snagem - Agrev - Marshtomp, Machoke, Shiftry, Ursaring (Dark 45)

You go to the leader's room and find Gonzap there again:

Snagem Head Gonzap - Armaldo, Machamp, Granbull, Crawdaunt, Breloom, Gyarados

You beat him and he'll storm off, swearing for revenge one day. You pick up the UFO disk U from his table.

Afterwards, you'll receive message about the Deep Colosseum in The Under. You head back there to compete. 4-battles per challenge again. You'll have to beat the thing 4 times (a total of 16 battles) and actually you'll battle the four Cipher Admins in the four final battles:

Bolta - Zangoose, Tropius, Nuzleaf
Yaruru - Vigoroth, Typlosion, Hariyama
Gekin - Girafarig, Hounder, Ledian, Dodrio
S.E. Miror B. - Exploud, Ludicolo, Ludicolo, Ludicolo, Armaldo

Misuruyo - Sneasel, Jumpluff, Electrode
Myo - Delibird, Marshtomp, Walrein
Marubo - Azumarill, Medicharm, Linoone, Xatu
S.E. Dakim - Nendoru, Flygon, Swampert, Solrock, Hhoundoom

Yodon - Machop, Ursaring, Machoke
Notten - Graveller, Wailmer, Wigglytuff, Donphan
Asuko - Spinda, Granbull, Delcatty
S.E. Venus - Blissey, Dusclops, Raichu, Meganium, Milotic

Ruzaa - Nuzleaf, Volbeat, Jumpluff, Agehunt
Hemato - Lantern, Exploud, Octillery, Lairon
Cofe - Marshtomp, Swellow, Crawdaunt
S.E. Ein - Electrike, Crobat, Gyarados, Mantine, Rhyhorn

Then you'll receive mail about Deep King owning a dark pokemon. You enter the Deep Colosseum challenge again, and the final trainer this time is Deep King:

Irun - Hhorsea, Nincada, Shuppet
Fedo - Misdreavus, Kadabra, Seadra, Kecleon
Una - Relicanth, Murkrow, Mawile
Deep King Zorudan - Girafarig, Skarmony, Sableye, Kingdra, Shuckle (dark 45)

After that, you'll receieve a message from the childrens network telling you they've recovered data for the last dark pokemon - Togetic. You pick up the Steel Teeth from the Deep Colosseum floor, give it to the old man in front of the UFO controller, and he'll give you the UFO disk L where you can get some items.

Later, you'll receive mails from people accusing you of hurting others with a dark Togetic. After some more mails and checking news on the TV as you move from region to region, you head back to the Outside-City Stand.

Outside-City Stand:
You find your clone standing there waiting for you:

Your Clone - Armaldo, Milotic, Houndoom, Magnectric, Gyarados, Togetic (Dark 20)

Turns out he's a Cipher grunt named Fake in disguise of you. You leave the stand, comes back and he's gone.

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