The thug finally runs off, having had enough beatings. The guards are taken out by Snagem, and you're free to go inside. The base is a labyrinth full of hidden Cipher peons.
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.
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.