A secret agent is a fanciful term referring to a spy. Secret agents are employed by espionage and intelligence agencies, many of which are directly associated with some form of government, but many may also be privately funded. A secret agent has the coolest job in the world. He or she gets to venture off to foreign lands, get into fist fights with terrorist scum and get to show off their fancy shmancy super-spy gizmos. Moreover, they ALWAYS get the girl! Even the girls seem to get the girl at times.
Some agents, like Colonel Steve Austin from The Six Million Dollar Man are employed by private institutions working to strengthen the country's security interests, but have the benefit of being able to operate free of government oversight. Other agents may belong to super-spy organizations such as S.H.I.E.L.D., which was America's greatest defense against terrorist threats as shown in Marvel's Agents of S.H.I.E.L.D. until it was revealed that they had been corrupted by the subversive terrorist organization known as HYDRA.