This sounds really dumb at first, but just read it all the way through:
The missing element is called Titanium. It is a mythical metal supposed to contain the essence of the gods. William manages to find some titanium (without knowing what it is) on his journey back home after the kidnapping, and decides to keep it, because he senses a strange aura. Then, when the wizard begins teach the party magic, William's magic is ridiculously strong compared to everyone else. He sees the stone glowing, explains where he found it, and then the wizard realizes it is titanium. Then, as the party continues to travel, they pick up many different types of titanium (maybe different colors, or just different appearance) with different magical effects. We could either put these in the accessory slot or make a weapon/armor upgrade system out of it.