It was, after the massacre and the metting with the Jowston Mercenary force led by Flik and Victor, that he returned to his hometown of Kyaro to meet with his family and reunite with Nanami. Jowy came to the gates of his estate only to be accused of spying for Jowston, and being disinherited by his father. It was there that Jowy found out that he was in no way blood-related to Marcel Atreides, that he, like Hero and Nanami, had been a nameless orphan. This was one of the single most traumatic instanced in his life.
Himself and Hero where marched off to be executed, and it was there that Jowy had a chance encounter with Jillia Blight, Luca Blight's sister. After having been led to the scaffold and horribly beaten, he was rescued by the Jowston Mercenary forces and the feiry Nanami. Bitter and hurt by what had happened, Jowy, along with Hero, went on many other adventures with Flik and Victor. They fought many more battles, and had seen much death and destruction.
It was after recieving the Black Sword Rune that the Wheels of Fate began turning for the young warrior. During a spying mission in a Highland Garrison and, after another chance meeting with Jillia, who had protected them for a time from the searching guards, Jowy was captured while defending the escape of Hero and Nanami. Outside the gates of Muse, the two faithfully awaited their friend's return until sunrise. During that time, Nanami talked of a similar situation where Jowy had sat on Genkaku's front steps and cried in the arms of Nanami, fearful over the disappearance of Hero in a nearby forest, and she swore that she would never tell another soul that he had shed a tear.
Jowy did return, but he seemingly wasn't the same Jowy that they knew and loved. He seemed aloof and secretive, and began talking to strange and shadowy individuals. In the end he was found by Nanami and Hero with a bloody knife in his hand, the lifeless body of the Mayor of Muse at his feet. Saying nothing, he fled out a nearby window into the darkness.
Little did they know that Jowy had a plan. So emotionally shattered was he by all the war and carnage, his father's coldness, his country's betrayal, and the senseless slaughter of the only adults that had ever been true parents to him, the parents of the tiny Pilika, that he would put an end to this senseless war. It did not matter that he would betray his friends and commit murder and make his heart like stone, but he would accomplish the task that was written behind the Black Sword Rune and the elusive message of Leknaat.