The war precipitated when Karnas's father was killed by Peretor Sain. In response, he took 63 passengers of a starliner hostage and asked Starfleet to give him weapons to fight his enemies and ultimately take control of the planet.
A Starfleet officer, Commander Mark Jameson was sent to negotiate with Karnas for the hostages' release. Instead, Jameson supplied Karnas with weapons in exchange for the the hostages, in blatant disregard of the Prime Directive. To even things up, Jameson gave the same weapons to Karnas' rivals, his interpretation of the Prime Directive.
Jameson falsified the reports to Starfleet and he thought that the fighting on Mordan would only last a year or two; however, his decision plunged the planet into four decades of war, which weighed on Jameson's conscience for the rest of his life.