It was sub-level, presumably below the basement. Lionel Luthor once referred to it as a redundant storage area.
In 2001, Earl Jenkins was assigned to that area when he worked at the plant as a janitor. Earl described an enormous cornfield being sprayed with a green mist— certainly meteor rock-infused fertilizer. He was caught in an explosion, and tiny particles of kryptonite penetrated his skin, causing him to suffer from random, violent seizures as his body tried to push the poison out of his skin.
Unfortunately, when Earl returns to the factory six months later, no one knew what he was talking about. All the employees who had known of Level Three were all transferred to Metropolis, so everyone Earl met thought that Level Three was a myth, like the Bermuda Triangle.
A few years later, Lionel still maintained Level Three experiments, such as cloning.
After Lionel was imprisoned, Lex took control of the operation. He moved the headquarters from the Smallville Fertilizer plant to a secret level in the LuthorCorp Plaza skyscraper in Metropolis, between Floors 33 and 34, and changed the name to Level 33.1.
- John Novack (Jed McNally) and Yee Jee Tso (Nick Yang) both appeared in an episode, of the BBC series Doctor Who (1996 film). Novack played the E.R. doctor and Tso played Chang Lee (The Doctor's companion).
- At some point, it's mentioned that there are/were Level Three facilities in Gotham City, Coast City and Bludhaven.
- Level 3 was basically Lionel's own 33.1 before Lex took over and making and changing it into his own.