The War of the Black Trees was a conflict between Dyrwood, the Aedyr Empire and Eir Glanfath in 2652 AI, 26 years after the start of the Broken Stone War and 171 years before the beginning of Pillars of Eternity.
In 2652 AI the Dyrwoodan troubles with their fercönyng were at a boiling point. Several of the erls under Edrang's rule, provoked by the imperial court in Aedyr resumed looting the ruins around Dyrwood that the Glanfathans held sacred. When the Glanfathans finally retaliated, it was overwhelmingly brutal and resulted in a slave uprising. Galven Regd, whom Edrang had fought before, resumed control of the Glanfathan troops. Regd was also able to convince some delemgan to join the fight.
Edrang was, at this point, far too old to lead his forces into battle, so he sent his son Admeth in his place to contain the threat. Admeth, true to form as the son of Edrang, and obviously having learned tactics from his father, made a dangerous, but effective, tactical decision. In order to prevent Regd's troops from using the woods as cover and to keep them from advancing through his land, he set fire to the forest at a tributary of the Isce Uar River and positioned his troops to prevent any of the Glanfathan forces from retreating. This tactic proved to be effective - while some Glanfathans and delemgan were able to escape, thousands died. In the skirmish that followed, Galven Regd was captured and sent to be held at New Heomar. Admeth was able to do what his father spent decades trying to do. He stopped Galven Regd.
Although the conflagrations generally benefited Dyrwoodan forces, the Glanfathans also made clever use of the burning forests from time to time. For example, Cas Raŵdha Dîal was a battle in which members of the Three-tusk Stelgaer tribe, lying in wait, charged out of a burning forest on the backs of their Stelgaer mounts, annihilating the contingent of Dyrwoodan soldiers that had thought its victory assured by its choice of tactics.
The conflict with the Glanfathans continued for several months, and Admeth repeated the scorched earth tactic several times to flush the opposing forces from key battlefields. He was able to bring the conflict to an end before the year ended. While it was a win for the Dyrwoodans, it was very costly as well, on top of consuming several thousand Glanfathan lives. Ultimately, however, the conflict would prove to be the last major war between Dyrwood and Eir Glanfath, with the devastation it wrought driving the two towards cooperation, rather than confrontation.
Like during the Broken Stone War, soldiers in the Dyrwood reported wild tales of having their minds invaded, of seeing comrades lose control of themselves, of orlan and elven Glanfathan warriors wielding knives engulfed in purple flames that "cut away" the souls of their victims. In the War of the Black Trees, Dyrwoodan animancers confirmed many of these experiences across a wide number of soldiers and settlers. However, with Dyrwoodan settlers in a state of war with the population of Eir Glanfath, the researchers couldn't find many Glanfathans who were willing to talk about it. In this war the Dyrwoodans learned that some old and large trees in Eir Glanfath have souls.