I know I'm being a little lazy but this article fails to explain just a wee bit what Fuel Cell Technology really is and why Apple would be interested in it.
I cannot say why Apple would be interested in it since I can't see it actually happening, but here is an example:

It seems suitable for a car but not for a phone. If I understand correctly, you have to give it liquid or gaseous fuel, and it needs air intake.
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You can run fuel cells on many fluids such as alcohols, hydrogen does not need to be supplied in its elemental form. As it is though all forms of stored energy have the potential to be dangerous. Plain old batteries can go into thermal run away, explode or other wise fail in hazardous ways. Gasoline is highly volatile but we use it daily. Even a tree is a form of stored energy and can get very hot when burned.
The advantage of the battery is that there is no possibility of its energy source to combust all at once. Also, you can charge it using electrical current.