 He served as CIA's Director of Congressional Affairs and as Deputy Inspector General.His tenure was on the research-analytical side, rather than the operational side; 
From 2000-2001 he was Deputy Director of the National Imagery and Mapping Agency (NIMA).In August 2001 Director of the CIA George Tenet named him the Chairman of the National Intelligence Council (NIC) 

In February 2002 President George W. Bush nominated Helgerson to be CIA Inspector General

As soon as he was in office Helgerson started an investigation into the then new program of CIA interrogations,following 9/11/2001.