The Cipher Key Lair is large and has thirteen Shadow Pokémon, so bring plenty of supplies.
Through the lair[edit]
You begin this mission by battling Thug Zook, who has a Shadow Zangoose with him. Catch the Zangoose and take out the rest with electric attacks. After the battle, head inside the Key Lair.
Inside, you can go in several directions. Go northeast to continue. Beware; trainers tend to fall from ceilings here, and you must battle one to reach the stairs. This trainer has two shadow Pokémon, so make sure you have one of your own out to support the team. Afterwards head upstairs to reach a Heal Machine. Take the stairs in the center of the room to continue up.
Push the boxes to reach the south side of the room. Take the stairs to continue to floor #4.
Work through the room clockwise to reach the roof, but first take the hallway you pass by to battle some more trainers and get the System Lever on the table. After you get it, go up the stairs to reach the roof.
Now that you're on the roof, go to the square thing in the center and battle the trainer there. Then examine the machine; you can use the lever on it. Turn it higher to make the door to the boss appear, but make sure to return to the Heal Machine first.
Inside the final room, take out the trainer with the Shadow Arbok and proceed to fight the boss of the Key Lair.
Cipher Admin Gorigan[edit]
Gorigan is a heavy user of the Earthquake/Protect combo, so make sure to bring any good Flying type Pokémon you have. Since Protect only has a 50-percent chance of working if used twice, he will usually have his Pokémon alternate between it. Use that knowledge to know who to hit each turn. Also, do not afflict his Ursaring with status conditions. Doing so will give it a drastic Attack boost. Also, his Sealeo has the ability Thick Fat, which halves fire and Ice type attacks you use on it; try elctric or fighting for a more effective attack.
Gorigan has a Shadow Hypno with him, so try to catch him. Don't try to put him to sleep since he has Insomnia. Instead, try paralizing him. While Electic type moves will hurt Sealeo and Slowking, bring Grass types instead due to their resistance to Earthquake.
After you win, check out the Shadow Pokémon List from Gorigan's desk, it will show you all the Shadow Pokémon that you're missing.
When you leave, head to Gateon Port and talk to Perr about getting the Robo Kyogre up and running. Doing so will allow you to reach the final area; Citadark Isle.