When Henry, his elder brother inherited their fathers titles in 1368, Thomas was probably in Spain fighting under the banner of the Black Prince, and on his death in 1376 Thomas transferred his loyalties to his son, Richard II. In his years of service under Richard he was rewarded with lordships in Wales and a number of castles and following his support of Richard during an attempted overthrow in 1397, Thomas was granted the title of Earl of Worcester.
Surprisingly, following the murder of Richard II on the order of Henry Bolingbroke in 1400 and his usurpation of the crown Thomas Percy did not suffer any consequences, in fact he was given a number of prominent position in Henry's court including Lieutenant of Wales.
Percy was still in this position in the spring of 1403, and we can only wonder if he had any knowledge of his nephew's grievances with Henry IV's rule. The discontent that Hotspur felt culminated in a rebellion against Henry and eventually his death at the Battle of Shrewsbury on the 21st July. The seeds of Thomas's part in the rebellion may have been set four months previously when the king replaced him as lieutenant of Wales, however he did remain in the kings service until the 17th, but by the 20th Thomas was riding with his nephew against the king.
History doesn't tell us why Thomas changed his allegiances, but it does tell us battles were won and lost on the actions of men like Thomas Percy - sadly in this battle all Thomas lost was his life.