1. Get the Cipher Key: You'll receive the Cipher Key from the Cipher Admin, Nitori, after you clear out the Cipher Lab on Route 219.
2. Go to the Abandoned Ship: Travel to Route 220 and then to the Abandoned Ship location.
3. Use the Cipher Key: The Cipher Key Lair is located inside the Abandoned Ship. Simply use the Cipher Key on the door to open it and access the lair.
You can do this even if you've lost to Zook and without defeating him at all. Zook's battle is not a requirement to access the Cipher Key Lair. The game actually encourages you to use the Cipher Key to explore the lair and gain an advantage before confronting him.
Remember: The Cipher Key Lair is a crucial part of the story, but it's not dependent on defeating Zook. Enjoy the challenge and the rewards!