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. It's that poor sap Smarton.
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.