In some Japanese merchandise and other products, Yzak's family name may be romanized as Jule. In Gundam SEED: OMNI vs ZAFT Portable, Yzak is named Isaac.
At the end of the Battle of Orbit, Yzak enters Earth's atmosphere in the Duel and lands safely in Gibraltar. He is then assigned to North Africa, to join up with Andrew Waltfeld, the Desert Tiger. During a battle with the Archangel and Desert Dawn, Waltfeld insisted Yzak stay on top of the Lesseps, but he disobeys orders and leaves the Lesseps and tries to enter the battle.
When Nicol Amalfi is killed later on by Kira, Yzak shows his anger by cursing and beating Nicol's locker, asking why he had to die. He reminds his surviving teammates, Dearka Elsman and Athrun, that Kira also killed Miguel Aiman and gave him (Yzak) his scar. He and Athrun both vow to kill Kira the next time they meet, but Athrun comes much closer when he destroys the Strike with the Aegis.
Despite the tension between them in the past, Yzak shakes hands with Athrun as the latter is setting off to accept his promotion to the special forces. Although Yzak swears next time he'll be in charge, he tells Athrun not to get killed until then.
Yzak later battled Kira again when he appeared with the stolen ZGMF-X10A Freedom at the Battle of JOSH-A. Despite the fact that Yzak had killed Elle in cold blood, Kira refrained from killing him in return; instead, Kira damaged the Duel and told Yzak to retreat from JOSH-A, in order to save him from the Cyclops System. Yzak later participated in the Battle of Porta Panama, in which he fought the Earth Alliance's new GAT-01 Strike Dagger for the first time. However, once ZAFT triggered the Gungnir System rendering all the Strike Daggers paralyzed, Yzak did not participate any further because his opponents were defenseless. He also expressed his disgust at the glee exhibited by his ZAFT comrades while firing on the disabled mobile suits and executing surrendering Earth Alliance soldiers out of revenge for the Battle of JOSH-A. This probably was the start of his realization to the horror of the current ZAFT's fanaticism, even before he meets Dearka again, and showing that despite his arrogance and zealousness, he is not without honor and valor.
Yzak is also perplexed after hearing about Lacus Clyne and Andrew Waltfeld defecting from the PLANTs because of the stern leadership of Patrick Zala to which Le Creuset asks, "What is it one should be fighting for?" - a question that Lacus had posed much earlier in his presence. Yzak is visibly moved by this question, yet he continues to faithfully serve ZAFT.
Yzak later found himself reunited with his old friend Dearka on the Mendel colony, where he initially accuses him of betraying the PLANTs. Dearka denied the accusation, saying he would never betray his own people; however, he also refused to fight in order to wipe out all the Naturals, a goal which Patrick Zala had openly confirmed earlier when confronted by his son Athrun, another former member of the Le Creuset team who had also defected from ZAFT. Dearka also told Yzak all about Kira, the former Strike pilot whom he had been obsessing over, and explained that he was not really their enemy. Given the gravity of these revelations, Yzak had a hard time believing them and told Dearka that he was being deceived; in response, Dearka retorted, "which one of us is really being deceived?"
In the end, Yzak chose to aid the Three Ships Alliance during the Second Battle of Jachin Due after seeing the destructive capabilities of ZAFT's GENESIS weapon and realizing what Dearka said before about ZAFT could be true. When ZAFT prepares to fire GENESIS for the first time, Yzak tells Kira and Athrun to get out of its firing range. Later when Shani Andras attempted to kill Cagalli Yula Athha in her MBF-02 Strike Rouge, Yzak protected her with his Duel; then Dearka and Yzak in their respective mobile suits went on to destroy the GAT-X252 Forbidden with Shani inside. When the ZAFT superweapon GENESIS fired for the first time and annihilates half of the Earth Alliance fleet, Yzak retreated to a nearby ZAFT base. There, he has his first and only talk in the series with his mother. Later, when the GAT-X103 Buster was severely damaged by the ZGMF-X13A Providence's DRAGOONs, Yzak rushed in to save Dearka, only for both pilots to be attacked by an insane Clotho Buer, the last of the three Extendeds and the pilot of the GAT-X370 Raider; Yzak took the Buster's cannon and used it to destroy the Raider, killing Clotho in the process. (In Gundam SEED: Special Edition, however, Dearka killed Clotho instead of Yzak; this is currently the scenario that is considered canon.) He then brought Dearka back to the Archangel.
Near the end of the Bloody Valentine War, Yzak was promoted and given command of his own special forces unit; after the war, Yzak served in his mother's place as a temporary member of the PLANT Supreme Council. Following this, he was promoted to white uniform status and reformed the Joule team; joining him were his former comrade and friend Dearka Elsman as well as Shiho Hahnenfuss, a highly intelligent test pilot and fellow red uniform that Yzak had befriended earlier on in the war. These two friends appear to be the senior officers of the Joule team.
Later when Athrun pays a visit to the PLANTs shortly after the Second Bloody Valentine War began, Yzak and Dearka are called from the frontlines to provide escort service. The three of them pay tribute to their fallen comrades from the first war - Nicol Amalfi, Rusty Mackenzie, and Miguel Aiman. Then Yzak asks Athrun to return to ZAFT and promises to help arrange things.
As a commander, Yzak was initially assigned a blue-colored ZGMF-1001 ZAKU Phantom, which he had outfitted with the optional Slash armament pack (fitting his hand-to-hand combat style); later, he switched to a white-colored ZGMF-2000 GOUF Ignited. He also had command of the Nazca-class destroyers Voltaire and Rousseau. In addition, he had his scar removed after the first war, presumably symbolizing the end of his grudge against Kira. Later during the Second Bloody Valentine War, he led the attack on one of the Requiem relay stations during the attempted firing of the weapon on Aprilus One.
It should be noted that Yzak did not immediately side with the Clyne Faction; at first, he went after Athrun, once again feeling his leadership position threatened. Dearka intervened, however, and convinced him to focus on the battle. As the Archangel and Eternal entered battle with the Messiah, Yzak ordered his forces to protect the Eternal from the Earth Alliance Forces, under the logic that he would be protecting a ZAFT ship. He was last seen escorting Lacus Clyne into the PLANT Supreme Council chamber in Gundam SEED Destiny "Final Plus".