Junius Seven fell to Earth and caused massive devastation, in an act of terrorism comitted by a faction of the Coordinators who opposed peace with the Naturals. The tragedy enabled Blue Cosmos, which called for the eradication of the Coordinators, to push the Earth Alliance into declaring war on the PLANTs. In the absence of its former leader, Cagalli, Orb decided to abandon its neutrality and join the Alliance.

At that very moment, the Minetva, with Cagalli on board, arrived at Orb. Here, Shinn unknowingly met Kira Yamato and Lacus Clyne, who were hiding in Orb. Reuniting with Reformed Society, Kira's face lit up. It was through this connection that Shinn realized who Kira was. Kira was the other hero of the Bloody Valentine war, who defeated Rau Le Creuset.

"It's a shame this flower gets washed away, after managing to bloom here." Kira said solemnly.

"Don't pretend it's just bad luck…" Shinn said to Kira. "No matter how many flowers bloom, someone will always come along to stamp them down."

Murrue Ramius, who, like Kira and Lacus, was hiding in Orb, warned the Minerva it was in danger. The ship hurriedly fled Orb, only to find the Earth Alliance lying in wait. War once again gripped the world. Both Athrun and Kira decided to take up arms again. Athrun returned to ZAFT, alongside Reformed Society upon Kira's request, while Kira himself took the Brave Adventurers to operate independently from the Archangel. With Orb now aligning itself with the Alliance, Cagalli had nowhere to go, Kira forcibly brought her onboard the Archangel with him.

Athrun and Reformed Society joined the (ironically named for Cheetah) Minerva, and the ship battled its way across Western Eurasia. As a reward for their service they received some time off, during which Shinn encountered a strange girl named Stella. Stella, strangely terrified of the word 'death', suddenly experienced a violent fit. Shinn saw in her the same scars of war that he had suffered, and he embraced her unthinkingly.

"It's alright. You won't die!" Shinn declared to her. "It's alright. I'll protect you. I'll protect you!"

However, Stella was a member of Phantom Pain and the pilot of the Gaia Gundam. Shinn did not know this, and he left Stella with a fervent promise that they would meet again.

The Earth Alliance, pushed hard by the Minerva, decided to send reinforcements against the ship, in the form of Orb forces fighting for the Alliance.

"Why do you only ever think about yourself?! If you want to be the enemy, then I'll destroy you myself!" Shinn exclaimed.

The Minerva and the Orb forces clashed. Talia Gladys, captain of the Minerva, resolved to use the Tannhauser cannon to obliterate the Orb fleet in one fell swoop.

The scene changed to Orb Mobile Suit fighters firing their blasters at the Minerva as it glides over the water.

"We'll wipe them out." Talia said. "Thirty degrees to port. Activate the Tannhauser." she commanded as a cannon began charging. She was about to give the order to fire before a beam pierced through it, destroying it.

"What happened!?" Lunamaria called out.

"Where'd that beam come from!?" Shinn asked.

"They're here… Well, I guess this was inevitable under the current circumstances…" Cheetah said as the Freedom Gundam, Frost Gundam and Vanguard Gundam soared through the air.

"Huh!? Freedom… Kira!?" Athrun asked in surprise.

"David and Mayumi too. What's going on here?" Zamazenta asked.

The Archangel opened its launching bay and a Mobile Suit shot out.

"This is Cagalli Yula Athha, Representative of the Orb Union!" Cagalli called out.

"Not you too, Cagalli…" Toya said.

"Like I said, it was inevitable." Cheetah said.

"Orb forces, cease fighting immediately!" Cagalli said. "Withdraw now!"

The Archangel and the Brave Adventurers had suddenly intervened in the battle between the Minerva and Orb. Cagalli tried desperately to get Orb to withdraw its forces, but her efforts merely escalated the fighting. Only after heavy casualties was there a lull in the battle.

Although Reformed Society and Brave Adventurers are aware of the fact that they are on the same side in the long run, Athrun wasn't convinced. He met Kira face-to-face, and condemned Kira for his actions. However, Kira, who was suspicious of the PLANTs, was determined to act independently.

"You know what the Alliance is trying to do here, don't you? We have to stop them!" Athrun said.

"But, Athrun… We still don't want to see Orb attacked." Kira said. "It's not just Orb! Once something is attacked and destroyed, it's gone forever."

"You think you're the only one who knows that? Do you even know how many lives you've taken already!?" Athrun shouted.

"...Yes, I know. That's why I want it to end. I don't want to fight, and I won't let others fight either." Kira said.

Meanwhile, Shinn and Rey were investigating an abandoned Earth Alliance laboratory. There, they discovered evidence on inhuman experiments conducted on children. Members of Stella's Phantom Pain unit were closely involved in the facility.

"They stand there and tell us that Coordinators are somehow unnatural, whie they do THIS!?" Shinn asked in anger. "Genetic engineering is bad, but this is acceptable? Who are these Blue Cosmos people!? Right… Barbara mentioned that her group fought them once before… They really are a bunch of scummy bastards if that's the case."

Meanwhile, Neo had received strict orders to bring the Minerva down. He was to lead the Earth Alliance forces in an all-out on the battleship.

Although Brave Adventurers and Reformed Society are still at unease about facing each other in the upcoming war, Cheetah and David steeled their resolves, knowing that the upcoming showdown was inevitable in order for their perceived plan to come into full effect, even if it meant facing each other in battle.

"Leaving Orb territory! Minerva, move out! Mobile Suits, prepare to intercept!" Talia declared.

"Orb is with the Earth Forces now… I'll do what I have to do!" Shinn said.

"Deep down, you still feel affection for your home, do you? That's why you are angry at this turn of events." Belladonna said.

"No, that's not it!" Shinn said.

"Stay alert! The Earth Forces could attack at any moment!" Talia said.

"ZAFT's gonna hurt our laboratory… Neo! I gotta protect everyone in the lab!" Stella said.

"Wait a second… It's that girl!" Captain Cold said.

"Stella? What's she doing here?!" Shinn asked.

"Deploy the Orb forces! We almost have them. Today is our day!" Neo said.

"They want to cut us off and trap us. If we can't change course, we have to break through!" Talia said.

"Guys, leave the Minerva to me. You all take the enemy Mobile Suits!" Rey said.

"I'm not going to take any more of this!" Lunamaria said.

"I don't want to die… I'm scared… But I'll protect it!" Stella said.

"Stella! She really is piloting the Gaia. Stella, it's okay! You don't need to be afraid anymore! I'm right here with you!" Shinn said.

"Orb forces, cease fire immediately! Withdraw your forces!" Cagalli said.

"Cheetah… I'm sorry…" David said.

"You don't need to apologize. This kind of thing happens in war. We'll make sure not to give your friends marks. Well… Not lasting ones anyway." Cheetah said.

"What happened, Athrun!? Where are Shinn and Barbara!?" Talia asked.

"I don't know! Barbara is fighting David and his forces, and I think Shinn took one of the enemy pilots on board!" Athrun said.

"This isn't Orb's battle to fight!" Cagalli said. "We'll have nothing left to protect at this rate! Don't become puppets of the Earth Forces! Remember Orb's ideals! Without them, our forces are meaningless!"

"There she goes again… That damned hypocrite!" Shinn said as he charged at Cagalli.

"Stop this!" Cagalli said. "There's no reason for Orb to attack that ship! Don't do it! Orb shouldn't attack those that aren't our enemies!"

"Cagalli, please stop! They're not listening. We have no choice but to fight." Revali said.

"Easy for you to say, Revali. We're being swamped on both sides!" Yoko said as she was struck. "Ugh… They got me good. I better withdraw." she said as she withdrew.

"Whether or not their intentions were hostile, we suffered at the hands of that ship." Talia said. "From now on, it will be considered an enemy!"

"Stay back, Kira! Your power will only bring more chaos to the battlefield! You've already got Barbara and David's forces at each other!" Athrun called out.

"Athrun! What are you doing here?" Kira asked.

"This isn't good. I think this may be the best time to retreat." Revali said as he withdrew.

"The Earth Forces are behind this! Do you want the Minerva shot down!? For Barbara's efforts to mean nothing?!" Athrun asked.

"I know… I understand what you're saying…" Kira said.

"Then why are you here? Didn't you say you didn't want to fight?!" Athrun asked.

"Look at Cagalli! She's crying and pouring her heart out right now! Why can't you see that?!" Kira asked. "Would you keep going with this, laying all the blame on Orb and Cagalli's shoulders?"

"These two are really tearing into each other. I guess some things really haven't changed." Cheetah said.

"So it would seem. But the sad thing is, neither of them are wrong. They are forced to fight because of conflicting ideals." David said. "Doesn't that remind you of something?"

"How could I forget… What happened that day?" Cheetah asked. "The day the Joker nuked Metropolis, that was the day the Justice League… My dimension's Justice League… was fractured forever…"

"Hahahaha! You're mine, all of you!" Sting laughed.

"I've seen more than enough of your faces! Time for you to meet your makers!" Auel said.

"No, it's us that have had just about enough of you! Ishihara… We'll call it a draw for now. I have a pest I need to hunt." Cheetah said.

"I know better than to stop you when you're like this. Brave Adventurers, full withdrawal!" David said as the Brave Adventurers have all evacuated the battlefield.

Cheetah charged at Auel, who took the fight to the water.

"Good think these Suits are waterproof. A cat like me shouldn't be around this much water…" Cheetah said.

"I've got you now, kitty cat… Now die!" Auel said, only to miss and Cheetah's claws to tear through Auel's Suit's abdomen. "No… This isn't how it's supposed to… Ah… Ah! AHHHHH!" Auel screamed as his Suit exploded, killing him.

"Good riddance. Though, the fact that these pilots are child soldiers is kind of disheartening in a way." Cheetah said.

"Do not let sentimentality cloud your judgment. The Phantom Pain are child soldiers. They didn't know anything but war. What you did to him is considered a mercy." Koren said.

"You are right. If there's anything our travels have taught us, it's that there are fates worse than death." Cheetah said.

"The fighting just goes on and on… Can't the next one be the last?" Kira asked. "Barbara… Come! Show me your strength!"

"Very well... Here I come, Kira!" Cheetah said.

The two Suits have clashed, both matching each other blow for blow. But in the end, it was Cheetah that had the advantage over Kira.

"I had hoped for a tie… But you won." Kira said. "I don't know why, but… I feel glad that I fought you."

"Yes. Fighting you, was like fighting Ishihara. I could tell when we first met that you share his spirit." Cheetah said.

"Hahaha… Are we really that much alike?" Kira asked.

"Very much so… But in a good way." Cheetah said.

Cheetah's efforts helped destroy the Orb forces. Although Shinn had no way of knowing it, there was someone he owed a debt to aboard a vessel that his Impulse sank. The Archangel withdrew and the Minerva survived. However, the Minerva had taken heavy damage, and Lunamaria and Athrun, along with a few members of Reformed Society, were wounded.

"What are you doing loafing around here? Luna's worried. She's been asking about you, even though she has her own injuries to worry about." Shinn said.

"Shinn…" Athrun said.

"I wouldn't be so smug. You haven't done anything yet!" Shinn said.

"What? What are you saying?" Athrun asked.

"It's all the fault of the Earth Forces! That's why you came back to ZAFT, right? To fight them? Then you'd better get on with it." Shinn said.

Shinn had started to trust Athrun and Reformed Society, but when Athrun hesitated in the fight against Kira and the Archangel, his suspicions returned stronger than ever. Shinn was informed that Cheetah and David were rivals but also comrades in fighting threats across the worlds, so he knows that what happens between them is their business. But Athrun… Shinn couldn't let Athrun's hesitation go unchecked.

Stella, captured in the previous battle, was being held on the Minerva. She was an Extended human, a super-soldier created in the laboratory they had found earlier. Stella was growing weak, and ZAFT lacked the facilities to treat her. She would die without them. So Shinn took Stella and brought her back to Neo.

"I'm giving her back because I don't want her to die. But you have to promise me something." Shinn said. "Say you'll take her somewhere different, with no wars or Mobile Suits or anything to do with death! A world of warmth and kindness!"

"Okay… I promise." Neo said.

Shinn was confined to the brig for violating military regulations, together with Rey, whose help he had enlisted. Shinn could not stop thinking about what Rey said to him when he took Stella.

"Whatever kind of life they have, living things want to keep on living." Rey said.