 Tom Welling feels that the deal Jonathan made with Jor @-@ El at the beginning of season three made Jonathan realize that he will not always be around to protect Clark . Welling believes that it is the repercussions of that deal that allow Jonathan to give Clark more freedom in the choices that he makes during season three . Jonathan realizes that he must help Clark find the confidence in his ability to survive on his own , so that he can leave home one day . One scene that Schneider specifically remembers was at the end of season three 's " Forsaken " . Here , Jonathan admits to not trusting his own instincts anymore and allowing Clark to rely on his . This " admission of fallibility " , but faith in his son 's ability to make the right choices , is what Schneider sees as the growing of the family dynamic . 
