Timotheo is the oldest son of the reigning Emperor of the Koryfonic Empire, Timos IX. Like other royal children, he and his mother are sent away from the imperial capital to live in obscurity, with the knowledge of his whereabouts and identity in exile kept in secret computers of the Emperor until such time as it might be his pleasure to name the appointed heir.
Unfortunately, Timotheo gets curious as to who his parents actually are, and does some research on his own. And this is a criminal offense in the Empire, for royal children at least, which causes him to be jailed and tried for treason. When he agrees that this is what he has done, although he doesn't see what's so wrong about it, he is found guilty and executed on the spot by his own father.
It's terribly cold-blooded, and terribly short-sighted too, and the Magid assigned to the affairs of the Empire, Deep Secret's protagonist Rupert Venables, is disgusted by the whole thing. It particularly bothers him since Timotheo appears to be a nice, intelligent young man who would probably make a much better Emperor than his father had ever been -- not as good as the famous Koryfos the Great, mind you, but a good Emperor, and instead his life was just wasted.
Timotheo does, indirectly, become the key to Venables' search for the other Imperial heirs, since his is the only name known to the harassed Magid, and it helps to unlock information in the Emperor's twisted, virus-infested computer files.
And since it turns out the the person who finally becomes the next Emperor is fated to be a very excellent one, things do turn out well in the end. Although not for poor Timotheo.