What would she be doing by herself? Welp, let's say Brian got offered a private mentorship back in Hoenn, but he agreed to help Mark and the others find out what happened. Thyme either offered or was asked to stay behind in his place. She would want to stay one, to do what she and Brian had promised, two, because of her friends, and three, Snype. but mainly cause she promised, and she doesn't want Brian's friends to get hurt, and because you don't turn down a professor when they ask you to be their aide, she stayed in his stead.