User blog comment:The Milkman/Indoctrination Theorists Say the Darndest Things, Part II/@comment-5830255-20121205094236/@comment-24174486-20121205175650

It's never explicitly stated that the Illusive Man's desire to control the Reapers is solely due to indoctrination. It's likely that the Illusive Man became indoctrinated through Reaper objects that he studied in an attempt to find out how the Reapers could be controlled. The Illusive Man's desire was to use the Reapers to bolster humanity's strength in the galaxy.