By by the 21st century, Khonsu was among the highest-ranking Tok'ra operatives, serving as an underlord to Anubis. Unusually for a Tok'ra, Khonsu held the loyalty of a cell of rebel Jaffa who knew his true affiliation, and who operated within the ranks of the loyalist Jaffa legion Khonsu commanded.
Whilst on an allegedly routine scientific mission, SG-1 was captured by his Jaffa and imprisoned by him. However, SG-1's capture was deliberate—a covert way of meeting him and obtaining information about how Anubis had been getting his advanced technology. The Jaffa Her'ak learned the truth about Khonsu and the rebel Jaffa working with him. Khonsu and his Jaffa Dol'ok were then executed by Her'ak as sholvas before SG-1 could escape. (SG1: "The Other Guys")