yes his dad went to jail somewhere in the town or outside of town they know Thomas is his son but seeing as the town is fearful of wolfponies so they have to punish him, a worst punishment could be far worst maybe death due to helping a "potentially dangerous" creature but again they don't know any better that they are not bad creatures.
now idk if Thomas will see his dad again, i plan that he does but maybe he will but i won't say when
so not much to say here really so i hope you enjoy this comic more will come soon