Complex sentence: McGehee figured he became the latest addition to the deputy's enemy list; he then thought that people like this deputy COS, who put his career above the mission, were "aberrations" among otherwise dedicated CIA agents.
Split into simpler sentences: McGehee figured he became the latest addition to the deputy's enemy list. McGehee then thought that people like this deputy COS, who put his career above the mission, were "aberrations" among otherwise dedicated CIA agents.