In 1995–1996 he led the counter-terrorism department of the National Intelligence Organization (MIT), which he joined as a student in 1965 as a "pursuit officer" (Turkish: takip memuru).
[9][10] Eymür prepared the controversial 1987 MIT Report that accused high ranking civil servants in the police and politicians such as Nevzat Ayaz, Ünal Erkan and Mehmet Ağar of having connections to the mafia.
[13] His colleague Hiram Abas, who was deputy chief of MIT and also discharged at the time, was critical of Eymür for divulging information.
[14] Eymür subsequently entered the ice producing business in Antalya with a MİT colleague called Korkut Eken, however this partnership ended after five years on acrimonious terms.
[7][11] After Tansu Çiller became prime minister in mid-1993, Eymür was appointed chief of the MIT's Special Intelligence Department (Turkish: Özel İstihbarat Dairesi) in May 1994.
[15][19] At the Counter-Terrorism Department, Eymür said he almost had the PKK's leader, Abdullah Öcalan, assassinated,[20] but failed due to irresponsible management of fiscal resources and sabotage (external, and inside the agency).
[22] Yılmaz said that the MİT strongly opposed Eymür's gang, and that such illegal activities now take place in the General Directorate of Security (police force) instead.
[7] Eymür prepared what has come to be known as the Second MİT Report (the first was in 1987), based on the "Askar Simitko, Lazım Esmaeili and Tarık Ümit incident" file from his Counter-Terrorism Department.
[29] From 2008 Eymür was mentioned numerous times in the Turkish press as being the superior of Tuncay Güney; the mysterious figure, who helped launch the Ergenekon investigation.