The Kaizoku faction developed originally on Arata Seken the homeworld of the Houjin people. They were ocean going pirates and smugglers. Hundreds of years later, when space travel was common and good were being shipped throughout the Houjin kingdom, they reemerged in 1462 A.D as an active threat to goods and lives. By 1470 A.D they were a major threat. Inaction on the part of the current Shogunate in crushing them immediately is what allowed them to become a major threat once again, a mistake the Houjin would not make again.
The Houjin navy along with the kingdoms armed forces fought with and pursued the Kaizoku with so much fervour that the Kaizoku saw they had to leave Houjin space to survive. See the tale of Gindoaw Hiati for more information.