Navigator Abson - Crawdaunt 33, Pelipper 33, Mantine 33, Golduck 33+, Sableye 33+

Then head into the volcanic mountain, and work around the first floor through random trainers with shadows. You will be stopped by Lovrina before you access the first elevator:

Cipher Peon Dimon - Masquerain 33, Dunsparce 33, Roselia 33, Spinda 33
Chaser Furgy - Zatu 34, Dodrio 34+, Whiscash 34, Raticate 34+
Sailor Toronba - Aron 34, Corsola 34, Pupitar 37 Hunter Ransa - Sneasel 34, Girafarig 33, Golbat 33, Seaking 34
Cipher Admin Lovrina - Gorebyss 36, Gardevoir 36, Roselia 37, Farfetch’d 36+, Altaria 36+

Defeat her and she’ll run off. Progress to the second floor now. You will find youself in a glass house like thing overlooking the stormy seas. Most of the researchers here won’t fight you, only the peons:

Cipher Beon Berd - Seviper 35, Crobat 35, Chimecho 34, Masquerain 34
Cipher Peon Litnar - Electrode 34, Misdreavus 34, Claydol 36, Kangaskhan 36+, Bannette 37+

Go up in the elevator again, and you arrive at the lava ground. Push off the white blocks to stop the lava flow, and dry up the ground to gain progress. You will be stopped by another peon along the way to the next elevator:

Cipher Peon Grupel - Houndoom 37, Ninetales 37, Vileplume 34, Magmar 36+, Pinsir 35+

Now go up the elevator and there are quite a lot of trainers to fight on this floor:

Cipher Peon Fajo - Stantler 34, Mightyena 35, Zangoose 35, Sunflora 35, Sharpedo 35
Hunter Ogera - Weezing 35, Forretress 35, Dodrio 37, Wobbuffet 36, Skarmory 34
Cipher Peon Kolest - Camerupt 37, Weezing 37, Muk 38, Rapidash 40+, Magcargo 38+
Cipher Peon Uumo - Cacturne 37, Ninetales 37, Torkoal 37, Mantine 37, Tropius 35
Chaser Carol - Dustox 35, Beautifly 36, Sunflora 34, Illumise 36, Volbeat 36
Rider Fego - Azumarill 34, Pelipper 36, Ariados 35, Octillery 36, Qwilfish 36
Cipher Peon Antol - Delibird 36, Grumpig 36, Swalot 35, Relicanth 35, Golduck 37, Quagsire 35

Two guards will be guarding the elevator, they fight you one after another consecutively:

Cipher Peon Karbon - Medicharm 38, Golem 38, Xatu 38, Hitmonchan 38+
Cipher Peon Petro - Skarmory 39, Grumpig 39, Metang 39, Hariyama 39, Hitmonlee 38+
Go up again, and there will be floating blocks around that you have to use to progress. Again, peons and shadows to snag:

Cipher Peon Koral - Roselia 39, Yanma 39, Smeargle 39, Vileplume 37, Altaria 40
Cipher Peon Akante - Banette 40, Sableye 40, Dusclops 40, Crobat 44, Wailord 44

Up the next elevator, and you will arrive at those coloured hooks where you are transported to each colour’s respective end. Work through the puzzle and gain acess to the next elevator after fighting some more peons:

Cipher Peon Gefta - Magneton 41, Lanturn 41, Lickitung 38+
Cipher Peon Leden - Stantler 41, Exploud 41, Scyther 40+, Chansey 39+

You should get to the top floor now, and the second Cipher Admin Snattle will come up from the other elevator to fight you:

Snattle - Metang 42, Quagsire 42, Scizor 42, Solrock 41+, Castform 42, Starmie 41+

Now with this elevator unlocked, you could get back to the ground without having to go through all the puzzles, but another peon guards the exit of this elevator on the ground outside:

Cipher Peon Metring - Shuckle 44, Blissey 42, Weezing 41

If you feel you’re ready, on the top floor, walk over to the dome shaped building, and on the bridge, you will be stopped by Verich’s blue bodyguard Ardos:

Cipher Admin Ardos - Swellow 43+, Alakazam 44, Kingdra 44, Heracross 44, Electrabuzz 43+, Snorlax 43+

Tough battle because he has three shadows. Beat him, and enter the dome-shaped building. Verich will compliment on your progress but then activates a glass shield to block you out. You head back out and before getting onto the bridge, the third Cipher Admin Gorigan appears from the other elevator close to the building to fight you:

Gorigan - Slowking 42, Ursaring 43, Aggron 43, Walrein 44, Poliwrath 42+, Mr. Mime 42+

Defeat him and like the other admins, he will flee. You know go down the elevator he came from, beat another peon along the way, and gain access to yet anoter elevator:

Cipher Peon Stron - Glalie 41, Ampharos 44, Breloom 42, Donphan 44, Dugtrio 40+

You will find yourself back in the room inside the dome-shaped building, this time pass the glass shield. Verich will go away and his red bodyguard Eldes fights you:

Cipher Admin Eldes - Ninjask 45, Manectric 44+. Salamence 50+, Flygon 45, Marowak 44+, Lapras 44+

Very tough battle again because it’s 4 shadows now, but be prepared and save here as the biggest nightmare is just a step ahead. There’s yet another elevator inside the room, go up, and you will instantly see Verich in the middle of the room. He compliments on all you’ve done so far in thwarting Cipher’s plans, but they have succeeded in creating the Pokémon that cannot be purified no matter what. He calls it the pioneer of their future shadow Pokémon team, and opens up the ceiling to call in XD001, Shadow Lugia.

You will first fight Shadow Lugia at level 50. Beat or snag it, then Verich will go berserk and fight you:

Cipher Boss Greevil (Verich) - Moltres 50+, Rhydon 46+, Articuno 50+, Exeggcutor 46+, Zapdos 50+, Tauros 46+

Toughest battle yet because you need to keep them alive while keeping youself alive. Beat him, and the ending animation will show.

The blue bodyguard, Ardos, reappears and curses you for beating their leader, then suggests blowing up the whole Citadark Isle. But Greevil doesn’t want to hurt his underlings and the researchers, and hesitates. The red bodyguard, Eldes, appears too, and says it’s immoral to do such a thing, and gets into a quarrel with Ardos. Ardos hollers that Cipher never dies, but Eldes claims that all is over, their factory is shut down, and even XD001 has failed.

While Greevil remains undecided, Eldes suddenly calls him father, and Ardos corrects him by saying that they should only address him as their leader. Eldes ignores him and tells Greevil that everything they’ve done so far is a big mistake. Ardos storms away, and Eldes holds out a hand to help Greevil up, saying that they should turn themselves in to the police. Greevil realizes that he is wrong, and Eldes comes to you, hoping to challenge you to a Pokémon battle one day without being enemies.

You walk out of the cave to see sunlight finally cracking in through the stormy skies, and light shines on every single city and town in Orre. Citizens rejoice in Agate, Phenac, and everyone cheers at the Gateon Port. You head back home where Jovi, your mom Lily and Prof. Krane congratulate you and welcome you back, and everyone that has helped you so far gathers at the Pokémon HQ Lab. The end credits then rolls.