Well, the overall plot sounds fine, but it would be good to have more of an immediate problem at the beginning to motivate the main character and stir up the player's emotions. How about, right near the beginning, the community of people who can't use pet monsters are forced to flee their town as refugees when the growing dark swamp stuff invades. Then you have the player's family as refugees, and the player will interact with them more because they will go with him to the first new location, and the player will be strongly motivated to reclaim their town, and thus to investigate the cause of this increasing problem. It would also bring the player into contact with the sky knights as the sky knights would be the reason that the second town the refugees go to is (temporarily) safe).
That could be interesting. It seems likely that other towns would be resistant to allowing the refugees in. After all, they're paying the fee to the "sky knights," and the refugees would just be "freeloading." Because of that, the refugees would likely end up sitting outside one of the towns, which means that they're partially under the knight's protective "umbrella" but still need the mentor's help to fend off attackers.
As far as contact with the "sky knights" goes, one of the ideas I had was that the PC would encounter an off-duty knight during the PC's first night in a protected town and would be challenged to a battle. Upon victory, the PC would probably get his/her first creature capture device. The knight may be impressed with the PC's potential and state that he/she could join the knights after becoming stronger. This would potentially open an avenue later for the PC to infiltrate the knights.