Strange Attractors — Jeffrey A. Carver

A SHIP FULL OF WORLDS

John Bandicut awakens, dazed, on the bank of a strange river. He and two humanoid aliens are stranded far across the galaxy, inside a vast "shipworld" that contains countless alien biospheres, all joined together in a wondrous web of energy and space/time. But, manipulated by powers beyond their ken, he and his new friends can't enjoy the marvels of Shipworld. Instead they feel driven toward a greater, unseen purpose.

Within Shipworld lurks an entity known as the boojum, which is corrupting the entire structure. Bandicut is inexorably drawn into battle with this evil, which threatens to destroy him and his companions, along with the enormous artificial world...