Every year between 2001 and 2013 (minus his time in Iraq with the 1st Armored Division in 2007), Thomas deployed to Afghanistan as part of various special operations units.

During that tour the division worked alongside Arabs and Kurds and despite the difficult relationship between the ethnic groups Thomas was praised by Hertling for "his ability to quickly fuse intelligence" adding, "He helped us fight better."

[3][7] Every year between 2001 and 2013 (minus his time in Iraq with the 1st Armored Division in 2007) Thomas deployed to Afghanistan as part of various special operations units.

[4] After commanding special forces units in Afghanistan, Thomas was promoted to lieutenant general and was reassigned to CIA headquarters in Langley, Virginia where he served as the Associate Director of the Central Intelligence Agency for Military Affairs.

[4] In a ceremony at MacDill Air Force Base, Florida, on 30 March 2016, Thomas took command of USSOCOM and received his fourth star.