We begin two years after the end of Gundam SEED, in C.E. 73. Serving as a part of PLANT's council until then, Yzak is promoted to a commander. With his own squadron and his own battleship, the Nazca-class Voltaire, he returns to the front lines when tensions once again start to rise between the Earth and PLANT after three new Gundams from one of PLANT's armories are stolen. Dearka is part of his squadron, assumed to have gotten demoted upon his reinlistment to ZAFT, though when not directly involved and in charge, Yzak seems to leave things to him, which gives the impression that in his own squadron, Yzak has him as more of a second. A group of extremist Coordinators who still believe in the views Patrick Zala held set up an attack on Earth. They go to the remains of Junius 7 and plant engines all over the colony, moving it out of its orbit and setting it on a direct course to Earth. ZAFT, and PLANT's new chairman, Gilbert Dullindal, sends the Jule Team in to break up the colony before it enters Earth's atmosphere. Set with such a huge task, Yzak orders his team to work swifty. They're joined by ZAFT's newest battleship, the Minerva in order to get the job done as quickly as possible. Yzak's team is attacked by the extremists group, and they try their hardest to get their job done as well as hold out the enemies and protect themselves. Yzak launches in his Slash ZAKU Phantom to aid his team.

Giving the order to keep working, or else they'd be giving the enemy exactly what they wanted, Yzak helps them defend against their attackers. But as they do so, the Alliance attacks them with the three new Gundams that they stole, and are pursued by the Minerva and their soldiers. The Jule Team manages and plant and set off a few of their Meteor Breakers, breaking the remains of Junius 7 into two pieces. A familiar voice rings out to Yzak from one of the Minerva's units, saying that it's not enough and they must break the colony into even smaller pieces. "Bastard, what are you doing in a place like this!" he yells back to Athrun, though he's glad knowing someone like him is there to help them with the operation. They continue their attempts to break up the PLANT through the still oncoming attack from the Alliance and Coordinator extremists. Yzak yells to Athrun to be quiet when he speaks, telling him that he's the commander now, so a civilian like him shouldn't be ordering him around. They get closer to the Earth's atmosphere, and the Alliance retreats. The Minerva decides to go ahead and follow the colony to the last possible moment in order to attempt to break it up more. They send Dullindal to the Voltaire, which falls back and remains in space, to escort him back to PLANT. Due to the Alliance as well as the resistance of the Coordinator extremists who caused the incident in the first place, they're unable to adequately destroy the remains of Junius 7, and it falls to Earth, causing mass destruction to the various areas around where the pieces fall. This begins the jump-start of the second war.

Due to the rogue Coordinators' actions, The Alliance launches an offensive on ZAFT after they deny demands to dismantle their military and dismiss their council, submitting to the alliance inspectors. ZAFT forces move into a defensive position, Yzak's team being one of the deployed squadrons. During their fighting, the Earth Alliance sends a second team from another area - this is their main offense, the soldiers currently engaging the ZAFT forces acting as decoys to give them an easy strike. This main offensive is equipped with nuclear weapons, and the moment he learns of their situation, Yzak orders his team to drop what they're doing and hurry to try and stop the attack in time. Yzak declares that they won't make it, but the team still desperately fires from the distance they're at in hopes that any of their attacks can make a hit toward any of the warheads. They brace themselves for a direct hit to their homeland's capital, but little do they know the ZAFT forces have a new weapon deployed -- ones specifically created to cause nuclear-powered weapons to detonate pre-emptively. Yzak is surprised about the new weapon, but glad that it worked and saved PLANT from demise. In the Gundam SEED: Delta Astray manga, the protagonist, a Martian named Agnes, joins this battle. When Yzak notices who he is, he tells him he's sent his information to the rest of his team, and that during the battle he'd be following his orders.

Yzak and Dearka are called from the front lines soon after the battle. They're given the assignment of escorting one of PLANT's visitors from Orb as he's requested to be able to leave his quarters (due to the start of a new war, supervision over those even from friendly nations is required). Yzak finds out it's Athrun, and when he arrives at Athrun's hotel, he's angry - lunging at him and yelling the moment he opens the door, demanding to know what the meaning of this all is. Athrun is completely lost, and Yzak explains their assignment, not hiding his anger over being pulled from the front lines for such a job. But there is an obvious reason why Yzak and Dearka were chosen for the assignment, as Dullindal is well aware of the camaraderie between the three during the first war. They ask Athrun where he wants to go (Yzak making the remark that he'd never forgive him if he says something like "shopping"), and he decides that while he was back on PLANT, he'd like to go visit the graves of Nicol, Rusty and Miguel since he hadn't in a while. They drive to the graveyard, paying respects to their fallen comrades and talking about the current situation PLANT and Earth are in.

Yzak fills Athrun in on ZAFT's point of view -- saying that they're asserting their right to self defense, and that couldn't be helped after they had nuclear weapons fired at them. Yzak asks Athrun what he, as well as Orb, plans to do, and then asks Athrun to return to ZAFT, offering to do what he can with his power in order to make it happen. In response to Athrun's hesitance, Yzak goes on to explain that he and Dearka should have died a long time ago due to their actions in the first war (Yzak destroying the shuttle full of civilians, Dearka defecting from ZAFT and joining the neutral faction), but were given a second chance by Dullindal. Dullindal pleaded for the soldiers of the first war, saying they were sent in to fight a war started by adults, and if they were all punished or killed because of their mistakes, there would be nobody to carry PLANT's future, and it was exactly because of the suffering and hardship they went through that they would be the ones who should create a peaceful future. That's the reason Yzak still wears his military uniform and does what he can for PLANT and his comrades who are gone. He tells Athrun that he needs to do something as well, and to not just let his power go to waste. In the Gundam SEED Destiny: The Edge manga, Athrun actually gives Yzak an answer and asks the two if they could go ahead, saying that he'll be back soon.

Most of the series's focus thereafter is on Earth, so there no information on what Yzak does during the time between Athrun's re-enlistment into ZAFT and Dullindal's announcement to the world about LOGOS. The announcement about LOGOS shocks the world as Dullindal explains that they are an organization that has been manipulating the world from the shadows, supplying weapons and benefitting from wars as a result. This throws many people into confusion, and frustrates Yzak. Passing a group of ZAFT soldiers soon after, he overhears them talking about the situation, joking about what Dullindal exactly plans to do, considering the circumstances of LOGOS's existence. He yells at them, telling them the situation is nothing to laugh about, and it's actually a bigger problem than many of them are assuming it is, a much more difficult one than simply fighting against the Earth Alliance. Asking if their heads are just there for decoration, he tells them to try using them before stomping off, getting a remark from Dearka that his own head looks about ready to explode.

Part of the Gundam SEED Destiny: The Edge Desire manga, "Partner," takes place at this point in time, as Yzak discovers the circumstances of Athrun's defection and alleged defeat. After learning more of Dullindal's true intentions, Athrun attempted to escape the ZAFT base he'd been stationed to, stealing a GOUF. The GOUF was reportedly destroyed by the Destiny Gundam, killing Athrun in battle. Yzak and Dearka look for as much information as they can following the incident but learn nothing more. Filled with regret and anguish, Yzak calls him stupid for doing whatever he wanted without talking to anybody else about it. Assuming Athrun is dead, Yzak and Dearka wonder if they're the only two left from their original team circa the start of Gundam SEED. Soon after this is the battle between ZAFT and Orb - started because of Orb's sheltering one of the LOGOS members, Lord Djibril, who is also one of the leaders of the Blue Cosmos. In this battle, the Freedom and the Justice, as well as the Archangel appear, fighting off ZAFT as Cagalli Yula Athha moves to retake power from Orb's current leaders who allowed Lord Djibril to hide there in the first place. The news shocks Yzak, who is still in space, and he becomes frustrated trying to figure out what exactly is going on. They wonder about the possibility that Athrun is alive, and though Yzak wishes he'd let them know if he were, he realizes that their position, as well as Athrun's being back with the Archangel, make it impossible. As he and Dearka talk about the happenings in Orb after Dullundal's fake Lacus Clyne, Meer Campbell is exposed, they get a message from the council...

The Jule Team is deployed to monitor a strange, cylindrical colony that's moving slowly toward the direction of PLANT. There are Alliance forces deployed around it, and Yzak and his team engage in battle against them. The odd colony stops its movements; a confusing move to Yzak. Lord Djibril, who had escaped to the moon, fires the Requiem, a giant laser that faces away from PLANT. However, due to the number and positions of those cylindical colonies, the beam from the powerful weapon is able to bend, and it hits PLANT, destroying six of them. Four from the beam itself, and two from impact from the hit colonies. The Requiem's intended target was Aprilius, PLANT's capital, but due to the combat around one of them, one of the colonies was set slightly off course, taking out the six instead. Just as the beam fires, Yzak realizes what's about to happen and screams for all of his troops to retreat. They move out of the beam's way, and watch helplessly as over one million of their people are killed due to the destruction of the six PLANTs. They're in a momentary shock, but Yzak quickly regains his composure and resumes command, calling out to team. He tells them that if it fires again, PLANT can be completely destroyed, so they have to take it out no matter what. The Jule Team resume formation and dive headfirst into battle again, taking out one of the colonies used for the Requiem.

The end of the Gundam SEED Destiny: The Edge Desire manga, "Partner," takes place during and after these events. During their attack on the colony after Requiem's first fire, one of the soldiers in Yzak's team, filled with anger about the situation, breaks rank. He's almost killed by one of the Alliance units and is saved by Yzak. When they return to the Voltaire, the soldier approaches Yzak, but before he can say anything, Yzak speaks. He tells the boy that he understands how hard it is to have to see something like what happened, but to not just strike out recklessly as a result of it because you can't protect anything that way. When Yzak leaves, Dearka reassures the boy, telling him that that was Yzak's way of telling him not to die in vain, because death as a result of a reaction like that is painful for everybody who considers him a comrade. Not long after the destruction of the PLANTs and Djibril's death, Dullindal announces his Destiny Plan to the world - an order that would assign every single human into a position that best fits the role based on their genetic makeup. Yzak hadn't heard anything about it before Dullindal's announcement, but doubts it's more than just a simple politial thing.

Then Yzak hears that ZAFT, after killing Djibril, used the Requiem to destroy one of the Earth Alliance's other stronghold bases. He's shocked by these actions, and scolds his own squadron when he hears a couple of them saying that they got what they deserved. He tells them that simply bringing everybody who defies them into submission by force isn't something that would just end a war, and that an idea like that is absurd. He tells his squadron that they're going to be returning to the front line, and thinks back to the first war - specifically, his own actions toward the end of the war when he rescued Dearka. Reflecing on it, he tells his team that the battlefield is a place where one can't tell what's going to happen. And that there will be times where you have to make decisions in the midst of the chaos, so at those times to remember why they're wearing a military unform and what it is they should truly defend. "Do you know what it means to be a ZAFT soldier? You have no regrets." With the Requiem now in ZAFT's possession as well as the Messiah (another GENESIS-type WMD), they are ready to overpower any who disagree with the Destiny Plan - namely Orb. The Freedom, Jutsice and ships in the neutral faction appear to stop them, and Yzak wonders how they are. Dearka suggests they go say hi.

Yzak orders the Voltaire to launch during the following battle, angry that nobody contacted him about what was going on. But as Dearka remarks to him, they're in ZAFT, so something like that wasn't surprising. As they get closer to the battle, Yzak wonders about some of the new mobile suits (namely, the Doms helping the Eternal), but Dearka interjects to ask him about what they're going to do. When he cracks a joke about launching and getting immediately destroyed, Yzak says that nobody should launch if they have that kind of thought in mind, and that he was launching to. He orders the captain of the Voltaire to stay supporting the rear and not to move out front, so they'll be safe and not get themselves destroyed. Yzak saves Athrun from an attack as they join the battle, and he angrily calls out to him, demanding to know why he's showing up again in this sort of situation. Dearka speaks up as well, noting that they're all aiming for the same thing so that doesn't really matter, and they should take care of the more important things first. Yzak and Dearka go with the Justice and the Freedom to destroy another one of the Requiem's beam-bending devices. The Messiah fires, taking out a great number of the forces that oppose the Destiny plan. As the battle turns desperate, Yzak orders that they're going to protect the Eternal, under the logic that it's a ZAFT ship. When the Messiah prepares another shot, it sends a message to all ZAFT troops to move out of its way. Yzak warns the Eternal about it, and says to tell everybody in its path to move as well.

The Requiem is destroyed, and soon after that, the Messiah is taken down as well. Lacus Clyne opens communications to the ZAFT forces, stating that there is no longer any need for the battle to continue, and requests that both forces agree to a cease-fire. The remaining forces from both sides do so, and in the time following this cease-fire with Lacus's help as a intermediary, returned to PLANT at the request of the Supreme Council. Leaving Dearka to control the Voltaire for her return, Yzak boards the Eternal to personally escort her back to PLANT. Some time after these events is where the Gundam SEED Suit CD 10: Kira Yamato x Strike Freedom Gundam drama takes place. Yzak and Dearka go to visit the graves of Nicol and the others on the anniversary date of the day Nicol was killed in battle. They run into Athrun there, and Yzak yells at Athrun, telling him that they had sent him a message that he never replied to to meet up. Athrun had gone on his own for the same reason without seeing their message. Athrun asks Yzak how work on the council is (since the war is over, Yzak returned to the council to help PLANT as he did at the end of the first series). Dearka mentions Yzak screaming in peoples' faces about GiNNs, and Yzak just states that he called them stubborn because they were stubborn, and that they were busy with so many things that they don't have time to focus on anything pointless. Athrun mentions that he got a recording of one of Nicol's piano recitals from his parents, though before they listen to it they talk about the wars and their comrades who were killed in them. When Dearka speaks about things, such as people like LOGOS still existing, he wonders if they'll always be stuck fighting and Yzak tells him to wake up, and asks him what he thinks they're doing now, and that he better not think that it's happening again because they want it to. He says he wants to do things right, for the sake of Nicol and their other friends. Before they leave and return to their duties to keep any more war from breaking out, they silently listen to the beautiful piano piece their old friend once played.

The Melancholy of Yzak drama occurs at some point after this. Yzak runs into Kira, who forgets his name and is promptly reminded of it, along with the fact that he's a commander. While Lacus is attending yet another meeting, Kira decided to wander around in search of someone under the impression he was getting an escort back to Lacus' house. An exasperated Yzak decides to be said escort to the, as he puts it, childish Kira who can't find his way anywhere. Kira tries to decline the invitation for help, which causes Yzak to assume Athrun must have said something about him. Eventually it's revealed that Kira heard from Athrun about Yzak being member #1 of the Lacus Clyne fanclub. And considering Athrun and Lacus had ended their engagement, Kira assumed Yzak was somehow involved and was now targetting him next, considering his relationship with Lacus. After Kira loses him, Yzak decides to head home and is met by holograms of different females, greeting and sweet-talking him. He approaches his mother, Ezaria, about this, who reveals that she set the entire thing up (and voiced each hologram) due to the fact that Yzak still isn't married or shown any interest in it, causing rumors that he may not even be attracted to women. She's also heard these rumors about his standing in Lacus' fanclub. And while she's sympathetic to the fact that Yzak is busy with his work in the military, this was the best way to prove both rumors wrong and find out what kind of bride Yzak would like the most out of the three hologram types. Unable to take this, Yzak quickly vacates his house and searches for the nearest ship to come pick him up so he can get away from his mother. The closest ship happens to be the Archangel, which Yzak begs to save him.