Lost Gate

The story centers around some "mages" who live in our contemporary world. They are descendants of the ancient Norse gods, but now live in isolation with limited powers. The typical powers tend to be a close relation with animals or materials (thus a stone mage could mold rock in to any particular form.) They have original come via a great gate from their distant world. However, an ancient mage closed all of the gates years ago. Any mage that starts to show gate-magery is quickly put to death.

So that brings us to a teenager who discovers that he is a gate mage - and thus runs away. He hooks up with some underworld figures, later leaving them to hook up with "orphan" mages. There is also a parallel story of another gate mage who "comes out of a tree" to participate in castle intrigue in a remote kingdom. Eventually, the teenager creates a great gate, and the tree man tries to close it, only to have the teenager defeat his closure.

The underlying magic is a slight variation of the system in Card's Alvin Maker series. It gets confusing at times; however, setting the fantasy in the contemporary world makes it much more accessible.