Chapter 2: In the Name of Justice, the Divine Thunder

Some of the crew assembled outside the Archangel, waiting to see if it really was Kira who had saved them. The boy walked down the hill to the assembled group and stopped a few feet away from Murrue and Mu, both of whom were standing in front.

He was wearing a ZAFT flight suit, a red one that would have signified that he was an elite pilot assuming he was part of ZAFT.

"I'm glad I was able to make it in time." Kira said.

"You're really … Kira?" Murrue asked.

Kira smiled at the question; doubtless, the crew was wondering just how he survived the final battle against Aegis. "Yes." He replied.

"Kira!" Miriallia cried out, rushing forward towards her friend. The rest of the crew followed suit except for Sai and Kuzzey, who took their time in walking.

He was assaulted with question after question but didn't answer. Instead, he stepped out of the group around him to meet his two friends.

"It's good that you're alive." Sai said, holding back the emotions.

"Yes, I'm sorry, but thanks." He turned around to face the crew again.

"It looks like we have a lot to talk about." Murrue said.

"We should get the Skygrasper and your suit recharged incase there's any stragglers." Kojiro suggested.

"Freedom doesn't need any energy." Kira said, eliciting stares from the crew. "It has an N-Jammer Canceller."

"So that means … it runs on a nuclear reactor?" Arnold questioned.

"Yes, and if you demand the data I'll leave right now. Freedom was entrusted to me to end the war and I will not betray that." Kira said almost menacingly.

Murrue nodded. "No one is to approach Freedom at any time unless given permission by Kira and Kira alone."

Kira nodded in thanks. Someone understood at least. They loaded the Skygrasper and Freedom aboard the Archangel and reconvened in the bridge after Kira had changed into his old uniform. Kira stood in front of the center window, looking down on the captain's chair. In attendance were Sai, Kuzzey, Miriallia, Murrue, Mu, Arnold, Romero and Chandra.

"Obviously the Alliance knew about ZAFT's operation for some time, the Cyclops system isn't the easiest thing to move around unnoticed. An operation like this would have required someone on the inside." Mu stated.

"It was the same up in the PLANTs. Everyone assumed the target was Panama." Kira replied.

"The next question we face is where we should go from here. Obviously, we can't return to the Alliance, we're guilty of going AWOL in the middle of a battle." Murrue proposed.

"Plus we knew about the operation, something like that wouldn't help us at all."

Mu added.

"Well for now we have to repair the ship. Crew dismissed." Murrue dismissed them. She and Mu went back to her cabin where Murrue sat in her chair heavily and sighed. Mu got two cups of coffee and set one in front of her.

"What about Orb?" Mu suggested.

"Orb?" Murrue repeated.

"Why not? They're a neutral nation and they know us, or at least the right people know us. At the very least we can take on supplies and give the crew a choice about their future." He reasoned.

Kira made his way back to his room and saw his stuff had been boxed up. A small metal cylinder on the floor caught his attention. He knelt down and picked it up; it was a tube of lipstick. Flay's lipstick. Memories of their last conversation replayed themselves.

"Kira … Kira, I"

"Sorry, we'll talk later, when I return."

The door opened and Torii perched itself on his shoulder. Kira turned and stood to see Sai in the doorway. "It was with me for some reason, and I didn't want to turn it off." He explained.

"Thanks."

"Well then …" Sai turned to leave.

"Sai." Kira said, and Sai turned to face Kira again. "Where's Flay?"

Sai didn't have the heart to tell Kira what she had said after the Archangel had reached Alaska.

"You knew it all along! All this time, I didn't have any real feelings for Kira!"

"Flay!"

"She was transferred when we were in Alaska, along with Second Lieutenant Badgiruel and Commander La Flaga. The Commander returned, but Flay and Lieutenant Badgiruel had already left."

"I see …" Kira dipped his head a little.

"I …!" Anger and sadness began to creep into Sai's speech. "I was saddened to hear that you might be dead! And now … well you're alive, and you've come back! I'm happy! But … why are you like that? We're different, but why am I different from you? Always … I can't stand being miserable when I look at you!"

"But, you're different from me as well Sai. What you can't do, I can, but what I can't do, you can." He explained.

Sai nodded in understanding and left Kira in peace. Not two minutes after Sai left Kira turned off the lights and flopped down on his bed, closing his eyes and sighing. The door hissed open again, letting the bright light from the corridor flood in.

"I guess they keep the lights off to conserve power." A female voice muttered.

Kira sat up at the sound of her voice. He knew that voice … but why was she here? "Flay?" he breathed quietly.

The lights came on with the press of a button, showing two startled people in the room. "Kira?"

"What are you doing here?" they both asked simultaneously.

Kira gestured for Flay to continue. "I thought you were dead." She stated.

"And I was told you'd been transferred at Alaska." He replied.

The two of them stared in silence for a minute before Flay spoke up. "I was going to go the mess hall for a drink, care to join me?"

"Sure."

"Archangel on final approach, speed 10, light is green. Call the ball." The Orb operator announced.

"Archangel, Archangel-class, formerly Earth Alliance." Arnold replied, slowing the ship to a stop and gently landing it while announcing the ship's name, class and place of origin.

Seven days after the disastrous events at JOSH-A, the Archangel was finally safely berthed inside the Morgenroete facility, with repair crews swarming out to begin fixing the ship.

Cagalli stood in front of the elevator, hopping from one foot to the other impatiently waiting for it to open. It finally did and she quickly moved to one side to allow medics and injured men off the lift first before ducking inside and closing the door. When it opened, she raced through the ship looking for Kira. She caught a glimpse of his head heading down a hallway and she called out his name and altered her course to get to him.

Kira turned in time to see Cagalli lunge at him, wrapping her arms around him in a hug that ended up knocking him to the floor. "You're such an idiot!" she cried out, tears streaming down her cheeks.

"Sorry Cagalli. I am alive." He simply said.

She got off of him and they stared to walk through the ship. "Athrun actually cried when he though he killed you. I wanted to know how he could even think about killing his best friend."

"War makes people do stupid things. He was almost justified in trying to kill me though. He never stopped trying to get me to join him, but then I killed his friend and comrade. In revenge, he killed Tolle. From there we tried to kill each other. And he nearly succeeded."

They stopped in front of Freedom. Cagalli stared at it. Even powered down it looked menacing and imposing. "What is that?"

"My means of ending the war. Lacus entrusted me with Freedom."

And ten days later, the repairs to the ship were complete, and the senior staff was asked to meet in the Morgenroete repair facility by Erica Simmons. Kira noted something in the dark against the wall but kept his mouth shut as he looked around the large bay. Mu, Murrue and Cagalli were all behind him, waiting for Erica to arrive, and oddly enough, Flay was beside him. Despite her former status as a noncom soldier, she'd been allowed to accompany them.

"Well, it's good that you're all here, I have a surprise." Erica said.

Powerful flood-lights activated, illuminating the back wall, revealing a fully repaired Strike Gundam standing tall and proud.

"Strike!" Kira exclaimed as memories of his last battle with Athrun ran through his head.

"ATHRUN!"

"KIRA!"

"We've finished the repairs and added an OS suitable for a Natural pilot, the same OS that you helped to create for our M1 Astray." Erica told them.

"So you're saying that anyone can pilot it." Mu said.

"Yes." Erica said happily.

"I'm going to pilot it." Cagalli announced, remembering one of her conversations with Kira over the Indian Ocean.

"All of this time you've fought alone on the battlefield, well no more Kira. I'm going to fight alongside you."

"Thanks Cagalli."

They all turned to stare at her with disbelief. "Err, with your permission of course, Captain Ramius." She added hastily.

"Sorry, you can't be the pilot." Mu said.

"Why not?" Cagalli demanded.

"Because, I'M going to pilot it." Flay cut in.

"Kira, I've spent my entire life having other people do things for me. Now it's time for me to step up. I'm joining the fight."

"Flay …"

Kira faced her. "No Flay, you're NOT going to pilot Strike." He growled out.

"And why not?"

"I don't want you getting hurt." Kira remembered Tolle had tried to defend the ship and his friends as well.

"TOLLE! NOOOOO!"

"So you DO care!" Flay jabbed her index finger hard into his chest.

"Look Flay … I don't think things can just go back to normal … everything has changed."

"Kira … what are you trying to say?"

"Now is not the time for this." He warned.

"Why not?"

"We'll discuss this later, but right now Mu is going to pilot Strike!"

The rest of them were surprised at the power behind Kira's voice. Who knew he could sound so commanding?

"Well until you decide, Strike will be here, waiting." Erica said and left the hangar. Cagalli ran after her, probably to talk about Strike.

Mu and Murrue left together, wordlessly, leaving Kira and Flay in the center of the hangar. The two teenagers stared at each other for a minute before Flay continued their conversation, or rather, their argument.

"Now why won't you let me pilot Strike?"

"Because … because you don't have any training, because you're only 15 years old, because Mu is more qualified, because it's up to Murrue, because …" he didn't add the last reason, knowing it would probably send the girl into shock if he did.

"Well, if I remember correctly, you're only sixteen years old Kira Yamato, and you piloted Strike without any prior training of any kind with mobile suits, and we're not part of the Earth Alliance military anymore." One by one, Flay shot down his seemingly flimsy excuses.

"I'm a Coordinator, you're not. I reprogrammed the first OS, you didn't. I made the second OS, you didn't." he desperately tried to think of more reasons to stop her, but none came to mind.

"So what, you're better than me? I thought you were different Kira, but it turns out you're just the same as every male alive." She turned on her heel sharply and walked out, leaving Kira to run his hand through his hair in regret.

The doors opened to allow Flay an exit and quickly closed after she left. He stared at where she had been standing. "Because I love you." He finally whispered.

Night had fallen before Kira returned to his bunk on the Archangel, he had spent most of the time either tinkering with Freedom or finishing a few things on Strike's OS. Erica had granted him and Mu clearance to Strike, and handed a pass to Kira to give to Flay.

"Just in case." Erica said, winking at him. Kira reluctantly took the pass and promised to make sure that Flay received it.

He was about to open the door to his quarters when he belatedly realized that Flay had moved into a different room after their chat in the mess hall over two weeks ago. His finger hovered in front of the button for a minute before he turned to find her new quarters.

Though it was late at night, Flay was just ready to turn in. The light was off, she had her shoes and stockings off, and her jacket was unzipped, showing the pink shirt beneath it. Her hand released her pony-tail and she shook her head to free the hair, running her hands through it as well.

There wasn't a chime as the door slid open, the hydraulics barely making noise. An outline of a figure was leaning against the doorjamb, his arms crossed. She didn't quite recognize who it was, but there were only two people she knew of that would barge into her room, and she was willing to bet hard cash that it wasn't Sai.

"You know," he spoke, confirming that it was Kira, "things fall apart, and they fall apart so quickly. You can't ever put them back the way they were."

"What do you want Kira?" she asked tiredly.

"It … it's just … you know, it takes time. You can't just have coffee and expect …"

"I know." Flay said, tears starting to well up as she thought about where Kira was going with this.

"There's just so much to work through. Trust has to be built again on both sides. You have to learn if we are even the same people we were. You have to learn if we can even fit into each other's lives, and it's a long and important process."

He walked forward, letting the door slid shut behind him. There was a soft glow from the vidscreen beside her bed. A single tear fell as he sat down on the bed beside her. "But what do they know?" he whispered in her ear.

Flay looked at him, not trusting her own ears. Kira smiled faintly. "You don't know how much I've missed you Flay."

"Kira!" Flay burst into tears, wrapping her arms around his chest, not wanting to let go.

"I'm here Flay, here for you." He told her, pulling her in close, stroking her hair gently.

She cried herself to sleep in Kira's arms, happy that he had come back. Kira could finally start to repay her for everything she had done for him. Morning arrived far too soon for Flay's tastes, but waking up with her arms around Kira and his arms around her was certainly a better way to wake up than most people would think of.

"Good morning sleepy-head." Kira teased, stroking her hair again.

Flay nuzzled into Kira's chest, not wanting to leave him again. He lifted her up to his height, their faces inches apart. "Did I tell you how much I've missed you?" he asked.

"Yes, but remind me." Kira gladly did so, their lips meeting in a soft kiss, the first they shared since their last visit to the Orb Union.

She finished their kiss, staring down into his violet eyes, reveling in the happiness they contained. It was the happiness that she caused him, the happiness that she was responsible for. In this moment, his happiness was all that mattered to her.

Flay leaned in close. "So does this mean you'll let me pilot Strike now?"

"No." she looked at him through narrowed eyes.

"And why not?"

"Flay, look at this from a logical standpoint: Mu is a veteran ace who has fought alongside me since Heliopolis. Now I have Freedom and Strike has an OS that can be used by Naturals. Strike may have the armor to protect you but you won't be able to bring out its full potential." He started to explain.

"Mu doesn't know how to use a mobile suit either." She pouted.

"That may be true but I repeat: Mu is a veteran. He knows what it's like to be out there fighting, especially against other mobile suits."

"What if we ask Manager Simmons if I could use an Astray?" Flay asked as the idea popped into her head.

"No."

Flay glared at him. This was starting to get really annoying. "Why not? Look, everyone starts out at the bottom at one point, and at least here I've got you, Mu and the rest of Orb to help me if I need it."

"Flay, I don't want you out there putting your life in danger." His voice lowered to just above a whisper. "I don't want to lose you, not again. We nearly lost each other but Fate was kind to both of us, and I would really rather not try it again. You mean too much to me."

Seeing just how much Kira cared about her was too much for Flay, as memories of how this all started came back to her. She had planned to use him for revenge, to turn him into a relentless killing machine, only for time to work against her. Now she felt the shame and guilt of her actions and what fueled them.

"Kira, there's something you should know."

"Flay …"

"No, I need to tell you. Why I did all those things, everything that has happened … it was all for …" she couldn't go on.

"All for revenge." Kira finished for her. She looked at him in surprise. "I know Flay, and I knew back then. Maybe I didn't realize it fully, or maybe I just didn't care because I was lonely, but I knew. And I forgive you, because you've changed, you've seen the errors of your ways, the evils that war brings about."

She burst into tears again because of Kira and his compassion, his understanding. He pulled her in close again and held her as she cried. Flay managed to bring her emotions under control just as a page came over the intercom system.

"Kira Yamato to the Morgenroete testing facility, repeat Kira Yamato to the Morgenroete testing facility."

"I guess that means Mu is ready to test the Strike. Are you going to come with me?"

Flay shook her head. "Sorry, but I've got a few things to do with Miriallia first." She dried her eyes and smile at Kira. "Thank you, for everything." She told him sincerely.

He drew her in close. "Anything for you." And he kissed her gently on the forehead before letting her go. "I'll be back."

"Kira wait!" she called out, grabbing his hand and pulling him into one last parting kiss on the lips, this one more heated than their first.

"Phase Shift active, all systems green, reactor running at 100 efficiency. I'm ready to rock and roll!" Mu confirmed.

"Roger that Strike, you are free to engage at will." Erica told him, as she and several others watched from the control room.

"I'm ready when you are Mu." Kira told him over a private channel.

"Good to know Kid." He looked closely at Kira's face on the screen. "Is that … lipstick?"

Kira immediately blushed and replied. "No … why would you think that?"

"Well I did rescue Flay back at Alaska so I simply assumed that you two managed to patch things up again." Mu said with a little glint in his eyes.

Kira was speechless. "Thank you Mu, I don't know what would happened if you hadn't done that."

"You owe me one. Fight hard Yamato because I'm going all out!" and he charged.

In response to the Alaskan Ambush, ZAFT attacked the Panama spaceport and mass driver. In an unforeseen occurrence, the Earth Alliance unleashed their newly created GAT-01 Mobile Suits, known as the Strike Daggers. Despite their efforts, ZAFT managed to drop a Gungir system down and set if off, letting the massive EMP wave destroy the mass driver and disable the Daggers.

In an instant the Earth Alliance had no way to escape into space …

A/N: There we go, changes! It will still follow the basic SEED storyline, but don't expect any copy and paste episodes anymore.
-Prayer