Disclaimer: I do not own Gundam Seed and Naruto

Kira Yamato was sitting in the cockpit of the Strike back in the Archangel just after destroying the Blitz with the Strike's anti ship sword. "I just destroyed one of them. I killed one of Athrun's teammates" thought Kira gripping the controls tightly

He looked at the cameras and saw all the mechanics cheering. "They cheering because they didn't just kill one of your friend's friends" thought Kira

Kira finally let go of the controls and opened the cockpit and got out of the Strike. While the mechanics were congratulating him and patting him on the back for a job well done pain shot though his eyes. Kira grabbed the side of his head while he still had his helmet on and pushed his way out of the crowd of mechanics and ran out of the hanger.

Mu saw Kira run out of the hanger holding his head and went over to the head mechanic and asked "What happened"

"Don't know, he just grabbed the side of his head and ran off" said Murdoch

In the pilot changing room, Kira was standing in front a mirror and took off his helmet. He was surprised be what he saw. His eyes changed color! They were now red and the pupil was now a tri bladed wheel. "What the hell" he shouted

He concentrated on his eyes and saw them change. The tri bladed wheel disappeared and a black pupil with three commas spinning around it appeared. "It changed" he said

He concentrated again and his eyes returned to normal. "Now it's gone" he said

Mu then ran into the room. "Are you alright kid" he shouted

"Yeah, I'm alright" said Kira

"What happened" asked Mu

"My eyes hurt a little but there fine now" said Kira

"Alright if you say so" said Mu

"Congratulations on finally getting one" he said as he left

"Thanks" Kira sighed

Later on

Kira was lying on a bed outside of the Clyne mansion in a gazebo after his big fight with Athrun. As he was sleeping he was having weird dreams.

A red eye with three commas spinning around it appeared with the word Sharingan under it.

Bits of information floated though:

The Sharingan is the Kekkei Genkai of the Uchiha clan.

The Uchiha is one of the two great clans of Konoha.

Konoha is the greatest of the five villages of the Elemental countries

He then woke up and looked around and saw Lacus standing near him. "I see you're finally up" said Lacus

Some time later

Kira and Lacus were outside in the gazebo drinking tea when Kira said "I have to return to Earth"

"Why is that" asked Lacus

"Something happened to me before my fight with Athrun. While I was unconscious I somehow learned where I could go to find out more about what I have now" said Kira

"What do you mean" asked Lacus

Kira closed his eyes and concentrated a little and reopened them showing his Sharingan. "What is that" asked Lacus shocked at seeing Kira's eyes change

"I don't know. This showed up before my fight and while I was unconscious I learned what it's called and where I can go to find out more about it" said Kira

"I see, but what will you do afterwards" asked Lacus

"I plan on going to Orb and try to find a way to help stop this war. I see now who it is I should be fighting against. It is the people who won't stop until the entire other side is dead" said Kira

"Very well then, I have something that would be of help to you" said Lacus getting up

"Follow me" she said walking towards the house

Later on

The Freedom just broke though the atmosphere and started heading towards Antarctica. Once he was nearing his destination the radar starting going off. "Why is it going off, there's nothing out there" Kira thought out loud

He then saw something shimmer in front of him before he past though it feeling a tingeing pass though his body. He looked back and saw ripples flowing though something before disappearing. "Was that a barrier" he thought

As he was flying over the continent towards Konoha he thought about the landscape he was flying over. "I thought Antarctica was supposed to be a frozen wasteland. But that down there looks like a desert" he thought

"I wonder if it has something to do with that barrier I went though" he asked himself

"But if it does, why wasn't I affected, was it because of that Sharingan thing I have" he thought to himself

The landscape changed to a heavily forested area and he knew he was getting close. As he got closer he saw smoke in the distance and thought "That must be Konoha"

But when he got there he was shocked at what he saw. "There under attack" he yelled out

He instantly targeted all of the giant snakes that were attacking the village and shot them. He watched as they went up in smoking thinking "Why or how did they do that"

He flew into the village and saw a giant sand beast off in the distance and took off to take care of it. As he got closer he saw that it was fighting a giant frog. "What's with all these giant animals" thought Kira

He put his gun away and drew his beam saber and cut though the sand beast's head and accidently killing the kid sticking out of its head in the process.

"What the hell is that" yelled a blonde haired kid in an orange jumpsuit standing on top of the frog's head

"I have no idea" said the giant frog

"Did that frog just talk!" yelled Kira in his mind

Thinking they could help him find the village leader, he turned on the Freedom's outer speakers and asked "Could you tell me where the village's government building is"

Shocked the giant machine could talk without a mouth he just pointed back to the village saying "It's the large tower in the village"

"Thanks" said Kira taking off towards the large tower

Deep within the blonde haired boy's mind, a powerful creature only had one thought going though it's mind "I can't believe they have become that advanced"

Kira spotted the tower and landed on top of it. He locked down the OS and set it to self destruct if anyone messed with it. "I hope it doesn't come to that" thought Kira

Once he touches down on the roof after getting out of the Freedom he was surrounded by armored men with masks on. "Hold it right there" one of them said drawing his sword

"Stand down" someone shouted

An old man appeared with white hair wearing a dark green shirt and pants with a red vest and a large scroll tied to his back. "Jiraiya-sama" said another of the masked armored men

"Why" asked the first one

"I saw him use that machine there to destroy the summon snakes that were attacking the village. And one of my summons just told me he also used it to kill Shukaku" said Jiraiya

"He actually killed a bijuu with that" yelled the second one pointing up at the Freedom

"That sand beast is called a bijuu" thought Kira

Jiraiya nodded his head and looked at Kira and asked "So what are you doing here"

"I came here hoping I could talk to your leader about something" said Kira

"The Sandaime fell in battle against the leader of the invasion but you could talk to the village council" said Jiraiya

"Alright" said Kira

Later on Kira was sitting outside the council room waiting for the entire council to arrive. Then another one of those masked armored men show up but this one looked to be female. "You may enter now" she said

"Thank you" said Kira getting up and going though the doors

He walked in and saw three groups of people. On the right were a group of normally dressed people. On his left were people who were dressed more like fighters. And up ahead were three old people. He also saw the white haired man from before off to the side. The old woman spoke up and said "Jiraiya informed us you would like to speak to us"

Kira nodded his head and the old woman said "Well could you remove your helmet to start with"

"Alright" said Kira taking off his helmet

"Very good, now please tell us what it is you wish to talk to us about" said the old woman

"Well back home there is a war going on. Even thou my country tried to stay neutral; we were pulled into it as well. After one of my battles where I have just killed one of the enemy's elite soldiers I got a headache and my eyes started hurting. When I looked at them in a mirror I found out they changed" explained Kira

"A doujutsu" was the thought that went though the entire council

"Could you please show us" asked one of the old men

Kira closed his eyes and reopened showing his Sharingan spinning. "The Sharingan" gasped out the council

"Are you an Uchiha" asked a man with pale white eyes

"I don't think so. I didn't even know any of this existed until after this appeared" said Kira pointing to his Sharingan

"Very well then, we will have an ANBU show you where you can stay until we can discuss this more" said the old woman

"I can't stay here! I only came to see what this was since there was a lull in the fighting. Once the fighting picks up again my country is going to need me" shouted Kira the Sharingan fading from his eyes

"Who said we would let you leave boy. We can use you to revive the Uchiha clan and take that machine of yours and use to crush our enemies" said the other old man covered in bandages

"I didn't want to do this" thought Kira as the seed exploded in his mind

The council was shocked in the sudden change in the boy especially in his eyes. "That will never work. Because I'm the only one who knows how to operate it and I set it to self destruct if any one messed with it. When it does, its nuclear reactor will go into meltdown and explode destroying this entire village and making this entire area inhabitable for centuries" said Kira while smirking

"But you will kill yourself as well" yelled out one of the normally dressed people

"Well, if I'm already captured I'll die knowing no one will have my machines power" said Kira

"Now, now, there's no need to do that. Maybe we could reach a compromise" said the old woman

"What sort of compromise" asked Kira

"What if you were to return here after the war in your homeland is over" asked a man with pineapple haircut

"I want to be able to go back home if they ever need me, I can't be forced to do what I don't want, and nobody touches my machine but me" said Kira glaring at the bandaged up old man

"That is acceptable" said the pineapple haired man

"Very well then I will be seeing you later. And hopefully when I come back you will have a leader that is not as greedy and corrupt as you" said Kira walking out of the room putting his helmet back on

Kira got back in the Freedom and turned off the self destruct and took off heading back from where he came. "Hopefully they will find a leader that can control that council or I'm going to be making a very short trip back" thought Kira

After Kira passed the barrier and was about to set course for ORB he heard a broadcast on the radio that was still set to the ZAFT frequency "The target of Operation: Spitbreak is JOSH-A Alaska"

"Alaska, The Archangel" shouted Kira as he changed course and blasted towards Alaska as fast as he could

Later on

On the space colony Mendel in Doctor Hibiki's personal office was Rau who was revealing Kira's true origins to him. "You are the dream of humanity, the Ultimate Coordinator" proclaimed Rau

As Rau kept on ranting the seed exploded in Kira's mind and his Mangekyo activating with the black tri bladed wheel turning purple. He looked Rau straight in the eye and said "Tsukuyomi"

A second later Rau screamed and collapsed to the ground along with Kira. After Mu made sure Kira was alright he went over and kicked Rau's body to see if he would get a reaction. He didn't, so he shot him in the head and heart to make sure he would stay down and went to see if he could wake up Kira. "Hey Kira, wake up" asked Mu shaking Kira's shoulder

Kira groaned as he opened his eyes and saw Mu looking down at him "Mu" asked Kira

"Glad to see you're awake. Are you alright" asked Mu

"Yeah I just feel a little drained" said Kira sitting up

"What happened back there" asked Mu as he helped Kira back up?

"What do you mean" asked Kira who was now standing

"Well one second Le Creuset was ranting and the next he screamed and collapsed along with you at the same time" said Mu

"I don't know, I remember getting angry and then everything going black and white and then nothing" said Kira

"Well whatever happened at least he's dead now anyways" said Mu

"Let's hurry back the others might need our help" he said walking out of the office

Later on

During the battle of Jachin Due as Kira watched the Archangel and the Dominion fighting each other, he saw an escape craft leave the Dominion. He then heard a voice he didn't want to hear again. "Archangel" shouted Flay over the radio

Kira activated his Mangekyo and targeted the escape craft and shot it. The beam went right though the seat where Flay was sitting.

Later on

After the war was over, in ORB, Kira was getting ready to go back to Konoha. He packed everything away in the cockpit behind the seat. He even was bringing some weapons he took from the ORB military seeing what kind of place Konoha was. "Do you really have to go" asked Lacus

"Yeah I promised I would return once the war was over" said Kira

"Be careful" said Lacus giving him a hug

"I will" said Kira returning it and slipping something into her pocket

"You better take care of Cagalli Athrun or I'll come back and practice what I learn on you" he said getting into the Freedom

"I can take care of myself you know" yelled Cagalli

Kira then took off and headed towards Antarctica. They then all left and went there separate ways. Athrun and Cagalli went to her estate and Lacus went to Reverend Malchio's orphanage. On the way there she felt something in her pocket and took it out. It was a cellphone with a note attached.

Lacus

I figured it would be best to give this to you since Athrun and Cagalli will be too busy with ORB. Call if anything bad happens and I'll come as fast as I can.

Kira

Lacus smiled and said "I will keep an eye on things for you Kira"