LL Dire. I am certain there are only two levels below ground under L1. the first level down - known as 'The Void' was used for cable and ducting runs (as well as certain nocturnal activities involving both sexes!!). Below that there are sump rooms and pumps for drain water and electrical switch gear. Also two rooms that had 15' diameter fans that pumped air round the building! There was also reputedly a fallout shelter that RAF were to be evacuated to in event of an attack. The truth behind this depended on who you asked - some said it did exist and others that there was no such place. Certainly I remember RAF bods trooping down stairs during anual exercise periods but I am reasonably certain there was no room with air and water supplies that could have sustained life for a prolonged period.
The OPS rooms were designed and built before terror attacks were thought of hence their proximity to the public road. After The Boys started throwing things that went bang they did put steel plates over the windows facing Porters Way as well as increasing site ingress security.
The RAF Linesman control rooms were on three floors in the tall L1 (Cathedral) block so they were blast proofed along with the equipment rooms at ground level in the other part of L1.
L2 was proposed for an underground site in Cheshire but the project got superceded by UKADGE.