I don't know how it will end, but I would love to see this:
So just as you deliver your finale spell and defeat Morganthe a cut scene happens. She stands there a bit scruffed up but in no way defeated. She says that she will not be destroyed by some student wizard. Then as she is saying this she begins to cast a extremely dangerous and powerful spell to destroy you. She casts the spell and when it looks like there is no hope for you Ambrose appears and deflects the spell like it is nothing. Then Ambrose and Morganthe have some dialog about the past and such. Then Ambrose tells you to step aside and that this is his fight. Thats when Ambrose and Morganthe throw down in a epic magic duel.
I think it would be cool to see the headmaster and his former apprentice go head to head. In the Malistaire Arc Ambrose stood on the side lines and let you handle it, but Morganthe is no small threat. Ambrose is the Headmaster for a reason so you know he is packing some serious power. Ambrose is also directly tide in to this story so I would love to see him participate in the end of this arc. What you guys think?