She disappears sometime after Duelist Kingdom and before battle city. She then turns against Jaden after battle city during the time of the oricalcos or however you spell it. Battle city is when he starts searching for her but helps Yugi in hopes that with all thats going on, he might find Yubel. And thats when Yusei comes in as well after stalking them a little bit to then confronting them and realize that he needs their help to fix the time line. Because Yubel disappearing wasnt suppose to happen. 

Trying to think of when Jaden should turn into the supreme King because of Yubel and Dartz but thats what i dont know yet.