The Under:
Sureddo tells you that most data has been destroyed but he'll try to sort something out. At the meantime, Siruba has gone off to investigate on the newly buily Realgam Tower. Sureddo tells you to head there for a look.


Realgam Tower: (previously the Constuction Site)
You enter Realgam Tower, fight Miror B. on the left room:

S.E. Miror B. - Loudred, Ludicolo, Golduck, Ludicolo, Armaldo
He'll give you the Red ID Badge

Right room:
S.E. Dakim - Forretress, Claydol, Flygon, Whiscash, Houndoom
He'll give you the Green ID Badge

You go in the front room to fight a Cipher battler:

Cipher Peon - Bareru - Dustox, Sludge, Seviper

Go left, then front, then two more Cipher battlers await:
Cipher Peon - Arton - Piloswine, Delibird (Dark 45), Glalie
Cipher Peon - Baila - Sunflora (Dark 45), Gloom, Jumpluff

Go further, fight Venus:
S.E. - Venus - Misdreavus, Bellossom, Raichu, Milotic, Wigglytuff
She'll give you the Blue ID Badge

Go right, right Ein:
S.E. Ein - Magnectric, Pelipper, Rhydon, Crobat, Starmie
He'll give you the Yellow ID Badge

Put all the badges on the wall of the room in between Ein and Venus's chambers and you'll unlock the door. Before you enter, you'll receive Rogan's mail, go back to him get Masterball.

Back to Realgam, go on and you'll battle another Cipher battler:

Cipher Peon - Dioge - Ariados, Masquerain, Heracross (Dark 45)

You then go on to enter a room full of trainers:

Rai - Nuzleaf, Graveller, Hariyama, Lombre
Charis - Octillery, Qwilfish, Seadra, Feraligator
Pain - Lairon, Metang, Mawile
Tirano - Wigglytuff, Loudred
Tres - Cradily, Swalot, Noctowl, Chimecho
Jack - Quagsire, Sandslash, Donphan
Shou - Machoke, Swellow, Ninetales, Magneton
Mystery Troop - Rosso - Grumpig, Muk, Breloom

You'll see Siruba in disguise standing in front of the elevator, he tells you to be careful. You enter the elevator and goes to the upper part of the tower. There you'll fight another trainer in the computer room:

Jack - Vigoroth, Shellgon

Then you see an animation of Nascour going even further up by another elevator. You give chase and Gonzap appears to stop you. He reveals to you that T.Snagem has been working side by side Cipher all along. He fights you:

Snagem Leader - Gonzap - Crawdaunt, Hariyama, Shiftry, Skarmony (Dark 47)

He then leaves and you and Mirei head into the 2nd elevator.
Now you end up in a Colosseum where thousands of people are watching from the bleachers. You fight 4 consecutive trainers before fighting Nascour.

Jonas - Porygon2, Zangoose, Miltank (Dark 48), (Exploud)
Delan - Absol (Dark 46), Grayena, Sharpedo, (Sneasel)
Cipher Peon - Nella - Houndoom (Dark 48), Torkoal, Magcargo, (Ninetales)
Cipher Peon - Ston - Tropius (Dark 49), Cradily, Vileplume, Cacturne, (Sceptile)

*You team gets healed automatically here

CipherNascour - Gardevoir, Walrein, Dusclops, Blaziken, Xatu, Metagross (Dark 50), (Alakazam)

Then the mayor appears from the elevator and walks up to you, revealing himself to be the boss of Cipher, Evice:

Cipher Head - Warudakku - Scizor, Slaking, Machamp, Salamence, Slowking, Tyranitar (Dark 55) , (Aggron)

Afterwards, the police cheriff Hejji, policeman Yuuto, Ginzaru, Siruba, Rogan all appear. Warudakku prepares to escape with a helicopter, but the Ho-oh's cry is heard in the sky and a sacred fire blasts down the helicopter. You tell Evice his evil plan is over now. Rogan says Ho-oh watches over the relationship between human and pokemons, and wouldn't allow such evi things to happen, and that you are now blessed by Ho-oh as it is a rare occasion to see Ho-oh so close up. Ho-oh flies around Realgam Tower and the end credit rolls.