The Regimental Return of June, 1862, which was held at Tupelo around the end of the month, makes note that he had died in the hospital at Grand Junction on June 17. How they derived this information we do not know.

It would appear that Thomas had died of disease or as a result of wounds received at Shiloh, Farmington or the siege of Corinth. We do not know, and there are no records extant of a hospital at Grand Junction. I should believe it being Grand Junction, Tenn.

Thomas J. Baker, Private, Company I, 21st Alabama Infantry, recorded on the June, 1862 Regimental Return as having died in hospital June 17, 1862 at Grand Junction, no other records

The regiment was in camp near Tupelo the end of June, 1862 where this return was recorded

M311: Compiled Service Records of Confederate Soldiers Who Served in Organizations from the State of Alabama

..........

The Twenty-first was mustered into service Oct. 13, 1861, at Mobile, and remained at Hall's Mill and Fort Gaines till ordered to Fort Pillow in March 1862. It remained there a few days, then moved to Corinth, where it was brigaded under Gen. Gladden. The regiment took part in the battle of Shiloh, where it lost six color-bearers in succession, and 200 killed and wounded out of about 650 engaged and was complimented in general orders. On the return to Corinth, the regiment was reorganized, and extended their enlistment from one year to "for the war." The Twenty-first was at Farmington,** but its casualties were few. In the summer the regiment was ordered to Mobile, and was on garrison duty at Fort Morgan, and at Oven and Chocta Bluffs.
http://www.archives.state.al.us/referenc/alamilor/21stinf.html

** Farmington, Ms, May 3, 1862