What is the relationship between SD-6 and the CIA?
 

It is very much a one-way relationship: remotely, the CIA monitors Sloane's movements within SD-6, with the help of undercover agents such as Sydney and Jack Bristow.

With the exception of very few high-level officers, no SD-6 agent has ever visited Langley, although Dixon, during the hostile takeover of SD-6 by "The Man", was successful in messaging the CIA for help using a hand-held wireless device.

Michael Vaughn at the CIA was notified, and made arrangements for a tactical assault against the terrorists; these measures were resisted by CIA Director Devlin as being out of CIA protocol. Despite this, Vaughn took direct measures, this time as a field agent.

The resulting counter-measures saved SD-6 from annihilation. None of the hostage agents, however, were to receive feedback on the success of Dixon's actions.