After defeating the guard in the lower-left, climb the stairs. Talk to the scientist in front of the control panel to initiate a battle.
After you beat him, insert the System Lever into the control panel and raise the voltage. The building will begin to shake. Walk back down the stairs and a Cipher Peon will come out of a door.
Heal, then go into the door on the roof and approach Gorigan to battle him.
Congratulations! After Gorigan is defeated, Greevil reveals himself on a video screen. He says that their main base and XD001 are on Citadark Isle and is protected by huge waves. After leaving the Cipher Key Lair, head to Gateon Port.
Pay a visit to the Parts Shop, and Makan and Perr will have a Robo Kyogre that can traverse the sea and reach Citadark Isle.