The Long War became inevitable as alchemy grew into science, and Sparks began to seize power from the prior feudal warlords. One might presume that a fear of "witchcraft" with the possible backing of a strong Church kept alchemic Sparks from gaining much power before. But as science and technology became the respected force, those who were able to wield it became the nuclei for new and sometimes fleeting series of empires.
As fascinating as the Spark and power both make people, Sparks who disagree make much more of a mess with "armies of giant carnivorous pea plants with ambulatory stalks" than do mere warlords. Minor offenses became inflamed, slights became major insults, and escalation of "my science is bigger than yours" led to the, as mentioned, inevitable.
When it actually segued from a long list of local squabbles to the actual War is unable to be determined. Eventually everybody was fighting everybody else; it made it easier on the historians, but not the peasants. Vast amounts of land were laid waste, and the hapless citizenry was recruited into Spark workgangs when they weren't fleeing for hopeful safety.
The Long War came to a pause of two decades when the Heterodyne Boys, whitest white sheep of their feared clan, took their places as heads of their House. Their self-declared mission was to clean up after the Long War, and with their powerful Sparks and the charisma that comes with that gift, they quelled the fighting and restored peace to much of the countryside.
The Other destroyed all their work, and also, seemingly, the Heterodyne Boys. Once the few remaining Great Houses' tattered genetic remnants crept out of hiding to find they were neither hunted nor restrained any more, they took up where their parents and grandparents had left off. Baron Klaus Wulfenbach returned from his mysterious exile to find Wulfenbach itself being rampaged over — the villagers massacred, the family schloss in ruins. Starting from there, he instituted the Pax Wulfenbachia (also called the Pax Transylvania on the model of the Pax Romana; or the Baron's Peace) — harsher than the peace created by the Heterodynes' charisma, less forgiving and quite heavy handed. But it worked .
At least for a time. A comment by Gil to Zola about the rule of Baron Klaus Wulfenbach, implying that the war is not finished, just quiescent ( ) soon proves to be prophetic: thanks to a combination of the various competing parties involved in The Storm King conspiracy, the returned Other, the fallout from the Siege of Mechanicsburg and random opportunists of every stripe, when Agatha emerges from the effects of the Timeskip, she learns that The Baron's Peace is a memory, and the Long War .