Sometimes, there's a job that needs doing that can't be linked back to the United States. Sometimes, there are situations where G.I. Joe can't get involved because of the ever sticky web of global politics. It's times like these that General Hawk calls up Shadow Ops, a section of the 'Joe team reserved for missions of an extremely delicate nature.
Where G.I. Joe is a Top Secret military organization, Shadow Ops doesn't even exist. Personally selected by G.I. Joe command for excellence in their given field, the members of Shadow Ops are individuals who choose to give up their identities to become anonymous instruments of military power.