He subsequently took the Oath of Allegiance to the Confederacy, in part to provide legal defense for Unionists charged in Confederate courts.

Those he defended during the course of the war included several members of the East Tennessee bridge-burning conspiracy and several participants of the Great Locomotive Chase.

[1][2] Young John initially worked as a merchant in South Carolina, but found it unfulfilling, and turned to the study of law.

[2] His political activities included ten years of service as a member of the North Carolina General Assembly, spread across three separate periods.

[2] By the end of his final term in the legislature, Baxter began seeking greater opportunities than Western North Carolina afforded.

On the advice of fellow attorney and Whig, Oliver Perry Temple, Baxter relocated to Knoxville, Tennessee, which lay across the Great Smoky Mountains to the west.

"[2] In describing Baxter's courtroom style, Temple stated that he quickly seized upon the key facts of the case, ignoring minor or insignificant points.

[5] Although a slaveholder, Baxter opposed secession during the sectional crisis that swept the South in the wake of the election of Abraham Lincoln in November 1860.

", which was published in the November 24, 1860, edition of the Knoxville Whig, Baxter called for a convention of delegates from all Southern states, believing it would provide an opportunity to calm the secession fervor in the lower South.

Along with Temple and ex-Whig leaders such as William G. Brownlow, Horace Maynard, and John Netherland, he canvassed the region to rally support for the Union.

[2] At the East Tennessee Convention's Greeneville session in June 1861, Baxter was a member of the Knox County delegation, along with Temple, Brownlow and Maynard.

While many secessionists, such as Landon Carter Haynes, welcomed Baxter's defection, others, such as Knoxville Register editor J. Austin Sperry, doubted his sincerity.

Shortly afterward, General Albert Sidney Johnston, at the request of Smith, arrested Baxter while he was on a business trip to Memphis.

Though he was released after a few days, Baxter angrily returned to a pro-Union stance,[5] charging Governor Isham G. Harris with orchestrating the arrest.

[2] In June 1862, Temple and Baxter provided legal defense for twelve Union soldiers facing court-martial in Knoxville for their participation in the guerilla operation known as the "Great Locomotive Chase", or Andrews' Raid.

Temple and Baxter argued the raiders were essentially Union Army personnel, not spies or saboteurs, and should therefore have been treated as prisoners of war.

[11] In 1884, Baxter overturned an injunction issued by a lower court that prevented baseball pitcher Tony Mullane from playing for the Toledo Blue Stockings, since he had already signed with the St. Louis Maroons.