Agate Village: (Pkmn Center, Shop, Berry giver, Celebi's Shrine)
In this village where great pokemon trainers retired at, you and Mirei go to her grandparents' house. Setsuma is the grandma and Rogan is the grandpa. Just as you were talking, a guy rushes in and informs Rogan that something is wrong at the Sacred Forest. Rogan rushes out and you follow.

On your way into the Sacred Forest, Cipher battlers fight you:

Cipher Peon - Hamiru - Carvanha, Spheal
Cipher Peon - Dain - Shroomish, Cacnea
Cipher Peon - Fami - Baltoy, Ralts, Kirlia

You enter and find Rogan's Pikachu defeated by another Cipher battler's Hitmontop in front of the shrine. You take over and battle him:

Cipher Peon - Skrub: Hitmontop (Dark 38), Wynaut, Geodude, Clampearl

Skrub flees and you head back to Rogan's house with him. He tells you to ask about Celebi and dark pokemons from the old guy living in the house close to the Shop while he finds the stone carving about the legend for you. You head over to the other old guy's house, learns that Celebi has the power to reopen the hearts of dark pokemons, and heads down to Celebi's Shrine again to pick up another Ein File titled C about the relationship of Celebi to dark pokemons and the need the destroy the shrine of Cipher to assist their evil plan. Then you go back to Rogan who now gives you the little tablet of the legend.

Just then, you receive a mail from Ginzaru who tells you to help out at Mt. Battle. You and Mirei head there.


Mt. Battle: (Pokecoupon exchange center)
You enter to find the place attacked by Cipher. You enter the battle stairs and fight 9 trainers:

Bob - Trapinch, Numel, Sandshrew
Dan - Baltoy, Swinub, Larvitar
Kathy - Sandshrew, Geodude, Numel
Zatt - Pineco, Baltoy, Hounder, Graveller
Mari - Lileep, Trapinch, Noveroach, Trapinch
Rua - Cacnea, Spinda, Kadabra
Yabun - Sandslash, Graveller, Vibrava
Cipher Peon Misa - Houndour, Duskull, Koffing, Kirlia
Cipher Peon Eje - Geodude, Geodude, Sandslash

Then you see another Cipher Admin, Dakim, hurting the area leader, Seniti, and he fights you:

Cipher Admin - Dakim - Metang, Golem, Swampert, Camerupt, Entei (Dark 40)

You Snagem Entei and he flees back to the lab. You pick up an UFO control disk F, then Seniti thanks you and gives you the Flute of Time, which is able to summon Celebi at the Sacred Forest. You head outside to fight one trainer:

Rei - Vulpix, Pikachu, [Abra]

You head back to Agate.