The Darkness Rune is the child of the well known Soul Eater. Surprisingly, your search for it outside the playing field of Suikoden 2 will be in vain. It uses two of the spells offered by the Soul Eater, Finger of Death and Black Shadow, although the latter is set as the fourth magic on the Darkness Rune. In addition to that, the Stealer of Souls is the first spell letting you absorb the enemies' health by command. An early crystal can be received by the time you face Neclord in North Window. In the course of the game, South Window's rune shop has it for sell, so don't worry about missing it.
Whether the Darkness Rune, considered as a normal element when it comes to damage calculation, is much of a help or not is another question, as there exist hardly any enemies weak to it, but a lot of them with a strong attribute for darkness. The rune itself is shaped like a scythe and remindes of its parent rune, longing for souls. - Celes