Thomas Waggener would have been born on the estate of his parents in Essex County, probably before 1720. He was apparently a career soldier, serving with at least a couple of the Virginia Colony Regiments. The first records show him as a Sergeant serving under Captain Beverly Robinson in his expedition against Canada in 1746 and 1747. This would seem to indicate that he had some kind of military experience prior to this. He next shows up on records as a Lieutenant with the Virginia Regiment in the spring of 1754. He served with George Washington in the apparent construction of and maintenance of Fort Necessity in 1754. His younger brother Edmund also served there as a Sergeant. Thomas was promoted to Captain in the summer of 1754. He fought with Washington in the Battle of Great Meadows (also known as Braddock's Defeat) on July 9, 1755. He was apparently wounded in this battle, and his brother Edmund was killed.
Thomas is listed on numerous records from 1756 through 1758. In 1756, under orders of Colonel Washington, he with a Company of 60 men, reportedly built and garrisoned two forts on Patterson's Creek. That same year he was also at the two forts at Fort Holland on the South Branch of the Potomac River near Cumberland, Maryland. He also is listed in 1756 at Monongahela, and he signed a petition at Cumberland. In 1757 He again shows up on records at Fort Holland and Fort Loundoun. In 1758 he is described in one record as being in command at Fort Pitt, and in other records as being at Fort Geroge and Fort Hopewell. Presumably, as a Captain, he was in command at many of these locations that he was serving at throughout this time period.
It is not at all clear what happened to Thomas after 1758. I have not found any records of him from 1758 until 1771. The indenture dated 1771 shows that he is clearly deceased at that point, but there is no indication of when or how he died. It has been reported that he lived to and fought in the Revolutionary War, but this seems very unlikely. There is no record of Thomas being married or having any offspring, and the 1771 indenture would seem to show that he apparently did not.