The Dragon's Apprentice (The Chronicles of the Imaginarium Geographica, Bk. 5)

Seven years after the events of "The Shadow Dragons," John, Jack, and Charles are finally able to return to their beloved Archipelago of Dreams. But even as old friends celebrate their return, new concerns shadow the reunion: the threat of Ecthroi, primordial Shadow. And perhaps even worse, the apparent splintering of Time itself.
Now the Caretakers must fight against their most fearsome enemy ever and attempt to restore Time, journeying through a forgotten Door from the destroyed Keep of Time in order to seek out the Dragon's Apprentice. Failure will mean the end of both of the worlds. But success will carry its own price - a price that may be too high even for the Caretakers to bear.