Yzak Joule graduated at the top of his class from the ZAFT military academy, granting him the right to wear the red uniform of an elite ZAFT pilot. Upon his graduation, Yzak was assigned to the prestigious ZAFT Le Creuset special operations team. His mother is a member in the PLANT Supreme Council, as are parents of the other elite pilots in the Le Creuset Team. Soon after his arrival, he was assigned to infiltrate the Orb space colony, Heliopolis to capture the Earth Alliance's new prototype mobile weapons. Yzak manages to escape Heliopolis with the Duel, and after the space colony began to break down, Yzak becomes the Duel Gundam's permanent pilot. Yzak, with the rest of the Rau Le Creuset team, continued to harass the Archangel and Kira Yamato, pilot of the GAT-X105 Strike.

During one battle Kira gives Yzak a scar on his right eye, and Yzak wears it as reminder of who gave it to him. Each time he battles against Kira he is unable to defeat him. After his meeting with Kira in the Freedom Gundam at the Battle of JOSH-A, he begins to question ZAFT, and eventually he aids the Clyne Faction during the final battle of the war.

Near the end of the Bloody Valentine War, Yzak is promoted and given command of his own special forces unit. After the war, Yzak serves in his mother's place as a temporary member of the PLANT Supreme Council. Following this, he is promoted to white uniform status and reforms the Joule Team, which now also includes his former comrade on the Le Creuset Team, Dearka Elsman. The Joule Team was involved in the unsuccessful attempt to prevent the Junius Seven Drop, as well as the pursuit of the next-generation Gundams stolen from ZAFT. As commander, Yzak is assigned a ZGMF-1001 ZAKU Phantom, which he had outfitted with the optional Slash armament pack (fitting his hand-to-hand combat style). In addition, he had his scar removed after the war, presumably symbolizing the end to his grudge against Kira. However, his soul still carries the scar of having murdered civilians in an impulsive fit of anger during the Battle of Orbit.