The Rift of Aln is a vast, deep fissure in a small corner located deep within the Emerald Dream, from which is thought by the druids that the Dream itself originated from. The druids also believe that it bleeds into the Twisting Nether and the Great Dark Beyond.
Gazing into it, Malfurion Stormrage saw it as a bottomless chasm which radiated with primeval energies that even he dared not investigate. Indeed, the very rift itself seemed half-dreamed, for it had a surreal quality to its expanse and to the archdruid now and then seemed to ripple as if ready to fade or change.
Curiously, only then did Malfurion truly sense that the ancient evil, though it fought to keep its grip there, did so from somewhere deep in the depths of Azeroth's own seas.
Malfurion and Tyrande Whisperwind cleansed the Emerald Dream everywhere, except in the rift where the Nightmare stubbornly held firm. There was no point to keep pushing, as the people of Azeroth still needed the couple's help. Thus, Malfurion sealed off the vicinity around the rift, he and Tyrande silently agreeing that the day had been saved, and this was another war that would have to wait for a better time.
The rift mentioned in the novel appears to be connected to the Rift in the Maelstrom. It may even be the same location, only as seen inside the Emerald Dream.