Hi! Thank you for your comments! Clock Tower was definitely an inspiration so it's awesome to see somebody pick up on that. Indeed the character originally in the bedroom is Nathanael, the protagonist's brother. Jebediah, the father, is the character in the cage in the library. We're hoping to improve the narrative and make it clearer in future updates because, as it stands, it is definitely a bit unclear (ambitious scope meets deadline ... casualties ensue).
Again, thanks for your comment, we're very happy you enjoyed it! Will be trying out your game later this evening - I am looking forward to it!