He gave the Avatar the task of clearing the seaways, and in return he would get the Codex of Ultimate Wisdom. However, the Avatar was double-crossed and arrested by Blackthorn. Samhayne however was innocent in that matter, and later helped the Avatar indirectly.
The Guardian kidnapped him and then killed him before the Avatar at Terfin. Samhayne told the Avatar about Raven's secret with his last breaths.
Samhayne was to have a much bigger role in the Bob White Plot, which was the original plot for Ultima IX. There, he essentially is another of the big players, actually having control over an entire army. He himself survives with everyone else on Skara Brae.