After Shinn returned to the Minerva, he repeatedly played battle simulations against the Freedom Gundam and the Brave Adventurers' Mobile Suits. Athrun protested but was ignored.

"The Freedom is the most powerful Mobile Suit I know. And those other guys look like they know their stuff. They even took down the Destroy. I had no idea a force like that exists outside our own sector." Shinn said. "Besides, someone in ZAFT has to know how to take them down, just in case. Who knows what they might pull next?"

"Yeah, but…" Athrun said.

Due to Athrun's past affiliation with ZAFT, he had become acquainted with the Knights of the Lost, and knew for a fact that David and the Brave Adventurers were capable of feats that someone with a mindset like Shinn's wouldn't be able to comprehend. Athrun was having trouble convincing Shinn of this fact, however.

"Athrun, I think Shinn has a point. It would be helpful if you could advise him based on your own experience." Rey said.

"That's fine, Rey. I don't need advice from losers." Shinn said.

"What did you just say?" Athrun asked.

Athrun insisted that Kira and the Brave Adventurers were not the enemy, but then, orders came down from ZAFT high command to destroy the Archangel.

"The Chairman said our enemy was Logos! So why are we going after the Archangel?!" Athrun asked. "These orders make no sense. Contact them again, and maybe…"

"I already did. The order is confirmed. The Archangel and its forces are already spreading chaos in the battlefield and escalating the fighting." Talia said. "I know you are concerned for Barbara and the others, but the existence of the Freedom and the accompanying force is a constant threat. We have no choice. The operation has already begun."

Athrun disagreed with Talia, but he could not defy his country's decision. Athrun became increasingly isolated on the Minerva.

Eventually, the ZAFT forces managed to surround the Archangel. Consumed by a dark lust for revenge, Shinn launched his attack. During Operation Angel Down, Shinn managed to destroy the Freedom Gundam. Although they could not confirm the Archangel's destruction, the Minerva's crew cheered at the elimination of their supposed biggest threat. Athrun alone did not join in on the celebrations. Seeing this, the triumphant Shinn confronted him.

"I got revenge… For the both of us." Shinn said.

"Why you…!" Athrun said before Lunamaria and some of the crew held him back.

"What are you doing?" Shinn asked.

"Does it make you happy knowing he's dead?! Are you proud?! Kira never tried to hurt you, and Cheetah and her friends have a lot of respect for all of those people! Revenge? Revenge for what?!" Athrun asked.

"You should be pleased. Our most powerful enemy is finally dead." Shinn said.

"D-Damn you…" Athrun cursed.

"What do you want me to do? Sit in a corner weeping? Pray for his soul?" Shinn asked. "Are you saying I shouldn't have taken him down!? Is that it!?"

"Shinn!" Athrun roared as he punched Shinn.

Gripped by rage, Athrun struch Shinn.

"Ungh! What did you do that for?!" Shinn asked.

"You know why, Shinn!" Athrun said.

"That's quite enough, Athrun!" Rey said getting between them.

"There was never any reason to kill him!" Athrun said.

"What are you saying?" Shinn asked.

"The Archangel, Kira… They weren't the enemy! And Barbara and the others… They left because of your callousness because they are still friends with Kira after the previous war! How could you just disregard their feelings like that?!" Athrun asked.

"What are you talking about? They were…" Shinn started.

"Enemies." Rey finished. "Whatever their intentions were, our nation determined they were enemies."

"Rey…" Athrun said.

"You don't get to decide that. We're ZAFT soldiers. Reformed Society left of their own will. That was their choice, and now they have to live with that choice." Rey said.

Rey's words struck a chord in Athrun, who realized the position his own choices led to. The rift between Athrun, Shinn and Rey could not be bridged.

However, Kira had in fact survived the Freedom's destruction, and along with Cheetah and Stella, were being treated on the Archangel. Neo was being held on the same ship, and tests had confirmed that he was in fact Mu. However, he had no memories of being Mu.

Meanwhile, Durandal's speech had won the people over. The enemy was no longer ZAFT, or the Earth Alliance. It was Logos. With this shift, Durandal gave Shinn and Athrun new power, in the form of new Mobile Suits… The Destiny Gundam and the Legend Gundam. Shinn was delighted by his new power and by Durandal's vision, but Athrun was growing increasingly suspicious of Durandal, who wanted everyone to play only the roles he assigned them. Durandal saw that Athrun could no longer be trusted to do his bidding, and ordered Rey to arrest Athrun for conspiring with the Archangel. At this point, Athrun decided he must break away from Durandal, just as Reformed Society did.

"I can't be his puppet, made to fight whoever he wants. Even if what he says sounds right." Athrun said.

With the help of Lunamaria's sister, Meyrin Hawke, Athrun fled the base with Shinn and Rey on his tail.

Shinn had been told only that Athrun was a traitor. Not knowing the real situation, he attacked Athrun's machine.

"Why are you doing this? Why?!" Shinn asked.

"Listen to me, Shinn! The Chairman and Rey, they say the right things, but their plan is going to destroy the whole world!" Athrun said.

"What?" Shinn asked.

"Don't be fooled, Shinn! Ask yourself, what are you fighting for!? The war is almost over, but you're going to throw everything away!" Rey said.

"Damn you!" Shinn said.

"Shinn! Listen to reason!" Athrun said.

"You're the evil one! You're the traitor!" Shinn said.

Athrun was overwhelmed by Shinn and the power of his Destiny Gundam. He narrowly escaped with his life and was rescued by the Archangel.

Elsewhere, Lacus traveled into space to try and discover Durandal's true intentions, but was intercepted by ZAFT. Kira launched into space to help, and received the secretly developed Strike Freedom Gundam from Lacus. Cheetah received a new Mobile Suit as well. Using parts that were salvaged by her battle against Razor in Jachin Due, Miu developed her new Gundam: the Apex Predator Gundam.

"Thank you once again, Lacus. Now Kira and I can fight again. Fight our own battles, our own hunts." Cheetah said.

The Logos leadership was almost wiped out in a Durandal-led attack, but their leader, Lord Djibril, managed to escape and went to ground in Orb. Durandal accused Orb of collaborating with Logos, and ordered a punitive strike.

"If Orb's gonna be destroyed, then I'll be the one to do it!" Shinn said.

The Archangel could not stand by and watch Orb be destroyed. While preparing for battle, Murrue released Neo.

"But why? What's going on?" Neo asked.

"You're not Mu. Are you?" Murrue asked.

Even as Neo left, Murrue's tears touched something deep in his heart.

Meanwhile, determined to protect her home homeland, Cagalli joined the battle in the Akatsuki, a golden Mobile Suit left to her by her father.

"This is Cagalli Yula Attha, launching in the Akatsuki!" Cagalli said.

"I guess I better go too. Sectonia, Queen Bee Gundam, launching!" Sectonia said.

"I am Cagalli Yula Athha, daughter of Uzumi Nara Athha." Cagalli said. "I hereby take command of all Orb forces! Do you hear me?!"

"Hmm… Doesn't look like it. Looks like we'll have to fight our way through." Sectonia said as she started to clear the field of enemies.

"Enemy stronghold in sight! Hit them with everything you've got!" Lunamaria said from the Impulse Gundam. "I hope I can handle this as well as Shinn."

"You may have a point, Sectonia. Pushing them back is the quickest way to a cease-fire! Do what you've got to do." Cagalli said as Sectonia quickly dispatched Lunamaria.

"Ouch… This wasn't supposed to be…" Lunamaria said.

"If Orb's gonna be destroyed, then I'll be the one to do it!" Shinn said.

"It's Shinn! And it looks like he's in a new Mobile Suit." David said.

"You people are not getting away this time. You manipulated Barbara and the others to betray ZAFT, and I'll snuff you out. All of you!" Shinn said.

"Doesn't that boy even know that Durandal is the one manipulating him?" Sectonia asked.

"Are you the one in command here? You can barely pilot that thing!" Shinn said.

"In my defense, it has been a while since I piloted a mech." Sectonia said.

"A while, huh? In that case, I hope you don't mind me taking you out right now!" Shinn said as he charged. "Now die!" he said as he tossed a laser sword at Sectonia before something brushed by and sliced it apart. "What the…?" he said as he saw the new Mobile Suit. "No way… This feeling… Barbara? What are you doing with them? Why are you on their side?!"

"Oh… Shinn, Shinn, Shinn… Did Athrun ever tell you?" Cheetah asked. "I always was on their side."

"Always? You mean you guys were conspiring with them from the very start?!" Shinn asked.

"Smart boy. You catch on fast." Cheetah said as Kira's new Mobile Suit appeared.

"Him too? But… But how? I killed you!" Shinn shouted.

"I guess you didn't check to see if he was really dead." Cheetah said.

"Well, this time, I'm going to make sure he stays dead!" Shinn said as he clashes with Kira.

"By the way, thanks for saving me back there." Sectonia said.

"What are you talking about? I was aiming for you! My… My mark was just a little off." Cheetah said.

"Really now?" Sectonia asked, unconvinced.

"Besides, Ishihara would be crushed beyond despair if you died." Cheetah said.

"Hehehe… Since when did you become so thoughtful?" Sectonia asked.

"Captain, I'm calling Shinn back. The situation has taken a turn for the worse." Rey said.

"Okay. I'll leave it to you. But hurry! You or Lunamaria will have to go instead." Talia said.

"Of course… Once Shinn is back. We need to shoot that thing down to win this." Rey said. "Shinn, get back to the ship, now!"

"What? Why? I'm not done yet!" Shinn said.

"That's an order. If you want to defeat them, retreat now." Rey said. "Lunamaria, you take the golden one and the bee Suit. Just keep them busy. I'll hit Orb head on."

"I'll open up a path. Mobile Suits, advance!" Lunamaria said.

"The Justice… So you think I'm just an ordinary soldier, huh?" Athrun asked.

"What I think doesn't matter. You're the only one who can decide that." Lacus said. "Power is what it is. You may well be a soldier, but you are Athrun first and foremost." she said as Mayumi and Revali soon defeated Rey.

"I've got to retreat and regroup!" Rey said as he retreated.

"Let's smoke them out! Target Orb's Nation Defense Headquarters! Fire!" Talia said.

"Guys, we need to stop that thing!" David said as he charged at the Minerva.

"This is Athrun Zala! Justice, heading out!" Athrun said.

"Enemy reinforcements… Is that the Justice?! Prepare to intercept! We'll give covering fire!" Talia said.

"Hope you don't mind me lending a hand." Athrun said.

"Much appreciated! Let's rock!" David said as the two of them start to clear the field of enemies.

"Djibril is getting away! We can't lose the ship. Pull back for now!" Talia said.

"I've got it, this time!" Shinn said.

"Keep a level head, Shinn. If you let yourself get provoked, you'll lose a battle you should have won." Rey said.

"This time, I'm taking you down, Frosty. And I'm taking Stella back!" Shinn said.

"Such a narrow mind you have." David said.

"Stop it, Shinn! Do you even know what you're trying to do!?" Athrun asked. "You're fighting Orb to get back at Logos. Is that what you really wanted?!"

"Yeah, man. Like, this place is your home, isn't it? Why are you so open to attack it like this?" David asked.

"Shut up! What the hell do you know?! You can never understand the rage I feel!" Shinn said.

"Actually… I do. And taking it out on us isn't going to change a thing." David said as he swiftly clashed with Shinn.

"Try to remember, Shinn! What was it you really wanted?!" Athrun asked.

"Shut up… Stop acting like you know me!" Shinn said.

"You don't know what you're babbling about! Don't listen to them, Shinn!" Rey said.

"Too late for that!" David said as he and Athrun defeated Shinn, just as Kira and Cheetah defeated Rey.

"The odds are stacked against us. We can't track him down. There's no point in continuing the fight." Talia said. "All forces, withdraw from Orb territory."

"They have called a withdrawal. Do not pursue." Cheetah said.

In the confusion of the battle, Djibril escaped in a shuttle to the Moon. When she learned this, Talia realized there was no longer any reason to continue the attack on Orb, and ordered a withdrawal.

"My orders were to capture Djibril, not to destroy Orb." Talia said.

Though she faithfully followed orders like the soldier she was, Talia was starting to doubt Durandal's methods. Cagalli, now in charge of Orb, also accepted the ceasefire. To Murrue's relief, Neo returned to her.

"I know you. At least, I think I do." Neo said. "I mean, I DO know you. In my eyes, my ears, my arms, I know you. That's why I couldn't leave. I know it must be hard for you, but it's hard for me too. So, please, let me stay here. Next to you."

Then Lacus revealed herself to the public, and warned the world about the true meaning of Durandal's plan.

"I do not support Chairman Durandal's words or actions." Lacus said. "The people who fight are not evil, nor the people who refuse to. The real evildoers are those who incite war. Logos, the merchants of death. The Naturals are not evil, nor are the Coordinators. He tells you it's THEM, not you nor the world. But don't be snared by his words. We must learn for ourselves the true nature of the world he is leading us towards."

Lacus and the others had discovered the truth about the peaceful world Durandal was aiming for. The Destiny Plan. A world where the genes you were born with would determine everything.

"This is the ultimate destruction for us Coordinators, who manipulated our fundamental genes to get all the power we desired." Kira said.

"People wage war because of hope, they fight because of desire. So let's get rid of hope, and desire." Lacus said. "Knowing what you can and can't do, can and can't have, from the moment you're born…"

"You'd know that from the beginning, because you'd know the genes you are born with." Athrun said.

"If this were to get out into other worlds, it would shake the entire Multiverse to its very core…" David said.

"Yes. It would completely change what it means to be human." Cheetah said. "Or any living being for that matter. You'd never have control over your own life, or anything going on around you. And obviously...we can't have that."

"That is the Chairman's peace. His world without war." Lacus said.

Man would not need to hope, or dream, or strive. None of it would mean a thing. Cagalli's bitter cry echoed through the bridge.

"It's impossible… But does that mean we give up?" Neo asked.

"Not me." Athrun said.

"Right. Me either." Murrue said.

"There's no way in hell we'd let this come to pass. It would go against everything we stood for." David said.

"Otherwise, none of us would be here in the first place." Kira said. "Let's head for space. All of us."

"We have to stop Durandal. It's not destiny that decides our future." Cheetah said.