Disclaimers:
I DO NOT have the rights to Gundam Seed, GSD, its characters, mobile suits and its setting. They are all property of Bandai and Sunrise. I'm just borrowing them for a bit. This is purely for enjoyment purposes. The original characters in this story are mine and they each got a little tag on them stating they they are mine.

Author's Notes:
I seem to be getting back to a normal writer's groove here as the progress of this story is exceeding my expectations. If I can get maybe two chapters posted a week at the most, then I think that's phenomenal even for me. I hope I can attract more readers to this story and get a review or two out of it.

In this chapter, The Organization discovered the identity of the young pilot who is currently in their care while the crew of the Archangel go into serious worry mode over the fact that Kira's mobile suit hasn't been found at all despite Cagalli trying her heart out to find him. The Archangel crew aren't the only ones worried about Kira. A certain Pink-Haired Princess is probably the most worried out of everyone.

In The Shadows

Phase 2: Awakening Of Dark Intentions

Lacus Clyne was anxiously awaiting any word about Kira Yamato from her friends on the Archangel. She could tell that something is horribly wrong from their silence whenever she tried to contact Murrue and the others in ORB. Whenever Kira went into any battle, Lacus instantly worries about him, just like any woman whose loved one goes into battle.

"Are you still worried about everyone on Earth?" Andrew Waltfeld, the Captain of the Eternal said as he entered Lacus' office on board former ZAFT assigned vessel. The ship was hiding as a giant rock next to the mobile suit factory where updated versions of the Justice and the Freedom were being built. She was hoping to give the machines to Kira and Athrun when the time is right.

"I am more worried about Kira more than anything else, Mr. Waltfeld. I know that the Archangel made it safely to ORB, but I just have this feeling that something bad has happened to Kira. And since Miss Murrue hasn't told me anything about Kira, I am beginning to fear the worst." Lacus answered sadly. Andrew could see the distress in the young lady's face. She really did care about Kira a lot and the feeling was mutual for him as well. Heck, he liked the kid as well, even though he lost Aisha in a major battle they had during the first Bloody Valentine War. Andrew never had any hard feelings towards Kira after that, already knowing the pain of war. Right now, the Desert Tiger was at a loss for words on how to make Lacus feel better.

I hope nothing terrible happened to you, kid. If you didn't come back to her, I'm not sure how well Lacus will handle it. Andrew thought to himself just as Lacus raised her head to make eye contact,

"That reminds me, Mr. Waltfeld. Why did you send DaCosta to that derelict colony nearby?" Lacus asked. Martin DaCosta is one of Lacus' staunchest supporters and one of the many ZAFT soldiers who defected at the end of the first Bloody Valentine War. He is also Andrew Waltfeld's trusted number two.

"There have been stories of Durandal using that colony for some sort of pet project he wants to implement on the people of Earth. So DaCosta is over there trying to find anything about Durandal's real plans." Waltfeld answered,

"Thanks to the information he showed the world about LOGOS, a lot of people on Earth are very trusting to the Chairman. And I have a bad feeling that he has mischievous plans for us and anyone else who opposes him." Lacus said,

"I heard it's becoming a real mess for the Earth Alliance and many of their forced defected to ZAFT in order to be on the right side." Waltfeld added,

"But there is no right side in this case. I have the darkest feeling that Chaiman isn't all that he seems." Lacus said. Waltfeld just nodded silently to her words. It would be a tough time for the forces against Durandal, especially since it is made worse by the fact that Kira Yamato might be missing in action. Or worse.

Back down on Earth, the Eliminator was closing in on the South American country of Val Verde. The crew was taking some time off to relax before they hooked up with their friends on the much bigger vessel, the Devastator. However, not all the crew were relaxing. The mobile suit crew were still busy working over the now dismantled wreck of a mobile suit formerly called the Freedom.

The Captain of the group was sitting in his captain's chair on the bridge as two crew members operated the helm and radar positions. The Captain was reading a few recent reports about the Freedom's capabilities when seconds later, Leeroy entered the bridge with a big smile on his face and an I.D. Card in his hand.

"Leeroy, by the look on your face, you must have found something big." The Captain said as the junior crewman handed the Captain the I.D. Card. The hangar crew found that in the wrecked mobile suit moments ago and Leeroy went straight to the Captain after he took a quick look at it.

"Oh, you're going to love what I found and you'll love who our special guest is." Leeroy said as he pointed to the young man who was still unconscious. The Captain took a look at the card and if he was drinking coffee, he would have done one hell of a spit take.

"Kira Yamato? We actually got the so-called Ultimate Coordinator on board?" The Captain exclaimed in surprise. Hearing the shocked and surprised voice of the Captain caused the two crew members to look at him in surprise just briefly before they quickly returned to their duties.

"The Ultimate Coordinator, Sir?" Leeroy asked perplexed,

"I will explain later. I have to see RLC at once. Take control of the bridge for me, Leeroy." The Captain said hurriedly and he quickly left the bridge, leaving a shocked Leeroy and the two crew members in stunned silence. RLC is the name of the organization's supercomputer that is housed in a special section of the Eliminator. RLC has the ability to predict an infinite number of outcomes in the missions the organization does and chooses the ones that have a near-perfect result for the group. Only the Captain has full access to RLC and once it makes a decision, its orders must be carried out at once.

"What was that all about, Leeroy?" The substitute radar operator asked,

"If I knew, I'd tell you Douglas." Leeroy replied to Douglas, the frail looking young man at the radar station.

"Since you're now in charge... what are your orders, Leeroy?" The substitute helmsman asked,

"Maintain our present heading and vessel speed for the rendezvous spot in Val Verde waters, Poochie." Leeroy replied to the substitute tall and dark looking helmsman nicknamed Poochie,

"Got it. Maintaining our current heading and vessel speed." Poochie replied as Leeroy sat in the vacated Captain's chair and took over as temporary captain. As he sat down, he began to recall stories about Kira Yamato and his ability to fight against overwhelming odds. If the organization was to reach its goal, then maybe using Kira for their own gains would work, but there is no way he would join them. Unless the Doctor did some surgery on Kira. Leeroy shook out that thought and focused on keeping Poochie and Douglas on the ball at they cruised to Val Verde.

Back on Earth, Cagalli Yula Attha was back on the Archangel reporting in on the fact that she couldn't find the cockpit of the Freedom anywhere. After over eight hours of searching she had to return because the Strike Rouge was running low on power and there was the risk of an attack by remnant ZAFT forces in the area. Without being able to find Kira, being stressed with worry is an understatement for her.

"I swear on the soul of my Father that I did not find the Freedom's cockpit anywhere, Miss Murrue! I looked everywhere I could with the Rouge, but the cockpit seemed to disappear!" Cagalli answered, totally distressed by the fact that the Freedom seemed disappear into thin air and taking Kira with it.

"You tried, Cagalli. That is the only thing we can ask from you. We'll think of something." Murrue said, trying her best to comfort the distraught blond haired girl.

"After hearing this, I surely hope I am wrong about what I said earlier." Neumann said, referring to his comment about ZAFT probably capturing the Freedom and using Kira for their own purposes. Surprisingly, the crew of the Archangel weren't in the mood to throw Neumann under the bus. Another problem was arising.

"I know we should be worried about Kira, but the rumor of the day is that ZAFT is planning a major attack on Heaven's Base in Iceland because it is the last LOGOS stronghold on Earth." Chandra, the Archangel's radar operator pointed out,

"Yeah, you're right. Plus there have been substantial reports of some Earth Alliance defecting to ZAFT's side for fear if they stuck by LOGOS, those forces will be branded supporters of LOGOS." Murrue said,

"I hate to be in their shoes right now with the entire world against them. It really seems like Durandal is achieving more than his predecessors when it comes to ending this war." Kisaka added,

"I know, but it seems like something else will happen to us. And it won't be good neither." Cagalli said. The crew of the Archangel seemed to share her concerns as well. Maybe they really are on the wrong side of justice. With each day, anti-LOGOS sentiments grew and support for Chairman Durandal grew as well. But there was one major concern the crew shared. Where is Kira and is he all right?

The small sick bay team were just finishing up a minor surgery procedure on Kira Yamato, whose discovery sent a shockwave of surprise around the crew of the Eliminator. While there was really nothing wrong with him, The Captain discussed the situation with the organization's super computer RLC and it told the Captain to have the medical team perform a minor surgery on the young man.

"I see you have already performed the surgery." The Captain said as he looked at the surgery team moving the young man into the recovery area for post surgery analysis.

"That is correct, Sir. Per RLC's orders, we have implanted the special tracking chip and if need be, RLC can remotely order us to change the chip's programming if he feels this young man can be of any use to us." The Doctor said as he was beginning to get out of his surgery scrubs,

"Good work, you guys. Did you get the sudden orders from RLC before you planted the chip?" The Captain asked,

"Yes. One of my aides read the orders and made the necessary changes to the chip. When he wakes up and doesn't remember anything, that means the chip is working to full potential." The Doctor answered,

"I really hate doing this to a young man we found, but we have to follow our doctrine." The Captain said. Moments later, Vincenzo entered the sick bay unit and noticed that the Doctor was finished getting out of his surgery scrubs.

"There was brain surgery and I missed it?" Vincenzo asked surprised. Anything bloody, gory and violent is one of the young man's interest. For reasons unknown, he seems to enjoy watching surgery operations.

"Yes, Vincenzo. There was tons of blood and he nearly died eight times." The Captain said falsely,

"You can't fool me, pops. The Doctor and his team are 100% professionals. I bet it went super smooth and there was minimal invasion of the dude's brain." Vincenzo said, like it was a matter of fact.

"Well, Vincenzo. If you're so interested in what is going to happen, we have just finished a surgery where we implanted a homing and health tracking chip in the base of his skull." The Doctor said,

"Wait, what? Are you going to lo-jack him?" Vincenzo asked,

"No, you idiot. We implanted the chip into his skull just to keep an eye on his vitals while we try to help him get back to where he came from." The Doctor lied. His last statement wasn't true, although the chip does function as a tracking device and keeps and eye on his vitals as well.

"Oh, Sure. I believe you. And I also know that there are some chips that can block memories and implant different orders for them to carry out in secret." Vincenzo said, almost suspecting the real reasons for implanting Kira with the chip.

"You must be reading too many science fiction stories online." The Doctor said,

"Hey, we have to do something to keep ourselves occupied until we hook up with the Devastator." Vincenzo said,

"You could have kept yourself occupied by finishing those damn reports you haven't turned in yet." The Captain said harshly,

"Well, I got another question. Why not pump him up with nanomachines and have them on the System like you did with everyone else? Better yet, why not make him take that disgusting crap you give me so I can go crazy and kill everybody? It's worse than that Red Bull shit that all of you worship. I swear they developed that shit from Red Bull." Vincenzo said,

"Red Bull is nowhere near the raw taste of Gamma Glipheptin when taken without a chaser. The only reason you hate Red Bull is because you threw up an hour later after taking it that one time." The Doctor said,

"The reason I puked that day was because the Iron Chef rejects we have in the mess hall used bad fish in the special that day. I haven't had fish ever since. And I used to love Fish 'n' Chips." Vincenzo answered,

"Look, Vincenzo. Just shut up for a minute. This young man is Kira Yamato, a.k.a., the Ultimate Coordinator." The Captain said as he pointed to the young man recovering in the ICU,

"Ultimate Coordinator? That kid? He looks a bit on the scrawny side if you ask me. I could break him in two like a twig." Vincenzo said as he looked at Kira's still sleeping form. He and Kira are roughly the same size, but Kira would most likely kick his ass in a fight.

"That 'twig' as you just called him, was one of the major protagonists whose actions ended the First Bloody Valentine War two years ago. People have said he's some sort of genius because he can easily re-write a complex operating system for mobile suits without thinking." The Doctor answered,

"So we got a brainiac on board. Can he outwit RLC in a chess match?" Vincenzo joked. The young man's constant sarcasm was now wearing thin on the two men. They can only tolerate so much of Vincenzo's crap before they try to kill him. However, the Captain was the cooler head and was hoping to end this nonsense.

"Shut up and listen to me, Vincenzo. Kira Yamato is also the brother of the current leader of ORB, Cagalli Yula Attha. He is also known to have access to powerful technology that he and his allies use." The Captain said,

"Cagalli Yula Attha? But she had blond hair and he's a brunette. So we're going to use him as leverage and make ORB do our bidding?" Vincenzo asked,

"I don't know, Vincenzo. RLC hasn't told me the specific details. I have to submit my report on the successful surgery to him before any other steps can be taken." The Captain answered,

"Have fun chatting with the computer, Captain. Derek wants me to help him inspect some systems the crew found on that suit called the Freedom. Maybe I can use some of them in my Duel." Vincenzo said as he left sick bay and the door slid to a close behind him. The two men gave out a frustrated sigh after Vincenzo left. There are those moments were Vincenzo nearly becomes a threat to the mission, but for some odd reason, RLC has told the Captain to keep him on the team. The supercomputer knows something they don't, so they are forced to tolerate the young man's constant annoyance.

"I think Vincenzo might be onto what we are planning." The Doctor said,

"Well, it really is no secret that those chips also have mind control capabilities that allow RLC to make people do the organization's bidding. In any case, continue to monitor the young man. We should be meeting up with our teammates on the Devastator sometime tomorrow." The Captain said,

"Orders understood, Sir." The doctor replied.

Closing Notes:

The Organization seems to begun their plans, whatever they may be. How they plan on using Kira with his memory blocked out is still a mystery. Only the supercomputer RLC knows the full plan, but it seems like Kira's friends have the right to worry. And what will happen when the Devastator and the Eliminator finally meet near Val Verde?

Please keep on reading and until the next time we meet, keep your mobile suit in tip top condition, make sure your Haro doesn't get wet and be ready to sortie in a moment's notice. And do drop a review or two if you like this story.