Disclaimer: I don't own Mobile suit Gundam SEED. Sunrise owns it; I'm just borrowing the characters and elements.

I hope guys enjoy this alternate version of the final episodes of Gundam SEED. I think a lot of you guys will probably launch a lot of flames at me. For the record, I HATE the Atlantic Federation, so please no flames on me.

Gundam SEED: Twist of Fate

Prologue: Beginning of the End

[Flay's POV]

"Archangel help, please Archangel!" I cried as I tried to figure out how to pilot the escape pod and get to the Archangel. "Please, ARCHANGEL!" I raised my voice loud enough for the fighting to stop as everyone paused to find where my voice came from.

[3rd person POV]

"What's going on? Who's that?" asked the leader of Blue Cosmos, Murata Azrael as he was confused by what just transpired.

"It's coming from ZAFT escape pod," answered the communications officer as they continued to here Flay Alster's voice, "We're picking up an international distress signal."

"Calamity, Ensign Sabnak, retrieve that pod," Lieutenant Commander Natarile Badgeral ordered Orga Sabnak.

"What?" Orga asked in disbelief that he would have to break off a wonderful fight he was having.

"Are you sure, we have no way of knowing that this a trap," observed Azrael.

"Yes, but she," began Natarile until she was cut off by Flay.

"I... I have something with me," interrupted Flay, "a key. The key that's supposed to end this war. So help me, please help me!"

Yzak Joule couldn't believe that his commanding officer was putting Flay in danger, in fact he was disgusted by Le Creuset's method of returning the girl back to the Earth Forces. He had no idea that Le Creuset was using Flay as the catalyst to ZAFT's destruction and would remain that way for a while.

Azrael then smirked as he was now curious about what Flay was talking about, this... key that was supposed to end the war.

"I wonder what she's talking about," Azrael said aloud enough for Natarile to hear him, "this key."

"So now, you really don't think it's a trap anymore?" Natarile asked Azrael sarcastically.

"Well doesn't it make you curious?" Azrael asked Natarile. "It's a strange comment to make. The words she used were 'the key that's supposed to end this war.'"

Natarile shot Azrael a nasty glare that would've killed him in a split second as she took it that Azrael had no regard for Flay's life but wanted this key.

'I just hope it's not something that'll give the Earth Forces the ability to use nukes once again,' thought Natarile. 'I've got a bad feeling that Flay might carrying something that the Archangel should take and keep out of the hands of the Earth Forces. I may not like Coordinators, but nuking them isn't humane at all.'

"Ensign Sabnak, hurry," Natarile urged the pilot of the Calamity.

Orga gritted his teeth as he broke off the fight and dashed off to retrieve the pod with the Freedom right behind him also going to retrieve the pod as Kira Yamato, the Freedom's pilot, recognized Flay's voice rushed towards the pod hot on the Calamity's tail. The Justice followed right behind trying to get the Freedom to fall back. Unfortunately, the Calamity's companions followed as well in order capture both the Justice and Freedom.

"Time's up!" exclaimed the pilot of the Raider, Clotho Buer as he was ready to pounce on the already vulnerable Freedom.

"You bastard!" added the pilot of the Forbidden, Shani Andras as he fire at the Freedom, damaging its head.

Clotho then fired off the Raider's mace knocking the Freedom's head clean off and preparing to capture it. Kira had been trying to talk to Flay but failed. Flay was certainly shocked and surprised to hear Kira's voice, let alone finally learning that he was still alive. Natarile was certainly surprised to hear Kira's voice as well.

"That voice, Kira Yamato, he's still alive," Natarile said aloud for Azrael to hear.

"Eh?" asked Azrael in confusion.

Within fifteen minutes, Flay was on board the Dominion and the Archangel had withdrawn from the area along with the Eternal and Kusinagi. She was led by an Earth Alliance officer to the bridge where Murata Azrael was waiting for her. Once the elevator opened, the Alliance officer allowed Flay to proceed to the bridge.

"Ah, so you're the girl," Azrael said as he floated towards Flay who was startled by Azrael approaching her. "Do you actually have it?" Flay silently handed over the disk to Azrael.

"Well it looks like you were telling the truth," observed Azrael as he looked at Flay. "Who gave it to you?"

"C-Commander Le Creuset," Flay answered Azrael nervously. "He wears a mask."

Azrael brushed past Flay without saying a word stuffing the disk in his left jacket pocket. Natarile was able to calm Flay down after she had cried in front of the bridge crew after being caught up in a terrifying situation that could've killed her. Natarile provided Flay with a white Earth Forces uniform so she could change out of the green ZAFT uniform she was wearing when she got back with the Earth Forces once again.

In Azrael's private quarters he looked over the information from the disk Flay gave him. What he saw on the disk made give off a maniacal laugh.

"Perfect!" exclaimed Azrael as he figured that he was given the key to wiping out all of the Coordinators and the Natural traitors and whores who sided with them. Flay however was going past Azrael's quarters when she heard Azrael giving off an evil laugh as she had a chill run down her spine and had a bad feeling that she just done something wrong.

Two days after the battle at L4, the Dominion returned to the lunar base at the Ptolemaius Crater on the moon and the crew was given plenty of time off for a successful job at L4 despite not acquiring the Freedom and the Justice. Many of the crew members were grateful for the time off as they went and enjoyed themselves doing their usual routines. Flay on the other stayed on the Dominion as she couldn't sleep after she handed the disk to Azrael.

Flay's POV

Earth Alliance lunar base, Ptolemaius Crater

'Why can't I sleep?' I wondered as I tried to go to sleep. 'I usually can sleep good, but I can't seem to shake this feeling that I did something something horrendous when I gave that Azrael guy that disk.'

Then I got up, put on my uniform and then sat on my bed as I struggled to decide on what to do. My struggle was on wither or not to risk my life and save the PLANTs or allow them to be destroyed. For some strange reason I saw two people that looked exactly like me. One had an Earth Forces uniform, had jet black hair and a ghost white face; the other one had a ZAFT green uniform and looked exactly like me.

'Come on Miss Alster, you should be proud that you are helping destroy the Coordinators after what they did,' my darkside said to me with an evil grin. 'They took your father from you and that liar didn't even make an effort to protect your father when he said he was going to protect him from those monsters. He's no different then any of the other Coordinators that deserve to be killed.'

'What have the Coordinators done to deserve death?' the part of me wearing the ZAFT uniform asked me. 'Even though Kira wasn't able to protect your father, he still fought to protect you and those around him. Even though you tried to get him to sleep with you just to comfort yourself.'

I lowered my head in shame as girl in the ZAFT uniform mentioned that. She was right, I had tried to get Kira to sleep with me and go a little further than just sharing the same bed just to feel safe. Captain Ramius had found out about what I tried to do and separated us because it wasn't proper military procedure. At the time I was angry that Captain Ramius had taken away the only means for me to keep Kira under my control. Only when Kira broke up with me did I start to understand what I was doing to Kira was wrong. I even tried to stop my continued use of Kira before I thought Kira got killed.

'That stupid Coordinator should've stayed dead and never come back,' my darkside said with venom in her voice. 'We were better off when you thought he was dead.'

'At least Kira came back and tried to protect you,' the ZAFT girl said to me with a small smile. I gave the ZAFT girl a weak smile back as I remembered hearing Kira call out to me trying to rescue me from the Calamity and its pilot, but had fall back because he couldn't fight anymore.

After an hour of both sides of my personality going back and forth, I made my decision and decided that I would help Yzak and save the PLANTs from being wiped out, even if it meant that I would be killed by Blue Cosmos for betraying the Naturals but I have to do this quietly and rely on my strengths.

Two days later

[Yzak Joule POV]

Martius One

I just can't stop thinking about that red head that was sent back to the Earth Forces. Part of me thinks that she should've stayed with us instead going back with the Naturals. I know it would've gone against what Mother and Chairman Zala are trying to do but former Chairman Clyne's attempts to make peace with the Naturals are starting to make sense. I'm starting to have doubts about ZAFT and the cause that we're fighting for. Man, I hope she's okay and hasn't been killed. [Shaking head violently] I can't be thinking about her right now, she's with the enemy again. I know I brought her home with a couple times whenever I had time off; Mother wasn't exactly thrilled about me bringing her home with me. ...I don't think it was much the fact that I was bringing a girl home, it was the fact that I brought a Natural home and someone who I thought was a prisoner. Mother was not at all pleased that I brought a Natural home with me and asked me why I didn't bring Shiho home with me instead. This had lead to an argument between Mother and I.

Flashback

June 29th, C.E. 71

Martius One

Joule Residence

"You shouldn't have brought that little Natural witch with you," Ezalia Joule, Yzak's mother said to her son. "Why didn't you bring that other girl; what's her name? Shiho Hahnenfuss, was it? It would've been better than this little whore."

"Don't talk about her like that!" Yzak snarled at his mother. "Besides there are Naturals living in the PLANTs. So why is the girl I brought home any different than any other Natural girl living here in the PLANTs?" Ezalia glared at her son before looking to Flay who had a worried look as she saw Yzak and his mother arguing.

"I-I'm sorry for causing any trouble," Flay stammered to Yzak and Ezalia as she slightly bowed and started to leave the Joule residence. "I'll just go back to the Vesalius until we have to depart for the next assignment."

Yzak looked at Flay as she slowly turned to walk out and head back to the Vesalius.

"Hey wait a minute," Yzak said to Flay softly. "Commander Le Creuset wanted me to get you off the Vesalius and that's what I'm gonna do."

"But me being here is only causing trouble for you and your mother," Flay said to Yzak as she looked at him and his mother who still glared at her.

Yzak just gave a smirk and said, "Don't worry about my mother. She gets like that when and if I ever bring a girl home. Trust me, the last time I brought a girl home my mother yelled at me for a month and drove the poor girl away because she wasn't the appropriate type of girl for me to date."

"I won't be any problem?" Flay asked Yzak in surprise.

"Nah," Yzak answered with confidence. "You're just gonna have to stay out of her way."

End Flashback

Damn, that girl was really cute and I probably could've convinced her to stay and not go back to the Earth Forces. I even had one of the Naturals' mobile suits repaired and a little modification done to it. I just hope she survives when the fighting stops.

Four days later

Flay's POV

Earth Alliance Lunar Headquarters

Ptolemaius Crater

The lunar base was certainly buzzing with activity as more shuttles were arriving with more mobile suits and troops as they were preparing for something big. I had no idea what was going on so I decided to find out myself. From the amount of mobile suits and troops arriving at the lunar base, I thought they might be preparing for an attack on the PLANTs and if that was the case then I would take action.

"The Sixth and Seventh Fleets will break orbit and make a direct assault on the defense satellite Boaz and PLANT homeland," a fleet admiral announced to his subordinates as I had evasedropped on the admiral.

'They're going to attack the PLANT homeland?' I wondered as I smiled at the Earth Forces' foolishness. 'That's really stupid. They're going to get wiped out by the Boaz Defense Forces. Although it's not much I should probably write it down and get any bits of info I can so I can warn Yzak.'

"I don't get why were attacking Boaz when we're going to get crushed," a mobile suit pilot my age said as I floated past him and his older counterpart.

"Shh, if any of the Blue Cosmos agents heard you say that," began the older mobile suit pilot, "they'd kill you on suspicion of being a traitor to the human race. Besides don't forget that we have those secret weapons to put an end to those space monsters."

"Oh yeah thanks to that one girl the Dominion picked up, that captive," the younger pilot to his older mentor.

The mentor gave a slight nod and then left the room they had snuck into with what I had apparently delivered to the leader of Blue Cosmos. The mobile suit pilot was still in the room and it looked like the appropriate place to use the same tactics I used to seduce Kira into doing anything I wanted him to do; it was isolated and I knew that I could take advantage of him. I entered the room as if I was lost and confused when the pilot spotted me.

"Hey there hot stuff, you know you're not supposed to be in here," the pilot said to me.

"But I need help," I told the pilot sweetly as I began to use my natural charms and poison on him, "and you're the only one who help me." In my mind I gritted my teeth and thought to myself, 'I'm gonna regret doing this.'

"How can I help you?" the pilot asked me.

The game began right then and there as I started to undo my shirt and started to show some features that made the pilot begin to blush.

"I need a strong man like you to escort me to my ship," I said seductively to the pilot as I continued to degrade myself a little further. "But you know life is short and you never what'll happen the next day." Before I could take my seduction to the next level, the pilot apparently fainted from being dumbstruck. Once he was out like a light I put my uniform back to the way it was before I almost gave a complete stranger my body willingly just to learn what I gave the leader of Blue Cosmos. I seemed to have some good luck as I found the information I gave the leader of Blue Cosmos. What I saw horrified me; I unknowingly just opened Pandora's Box and gave the Earth Forces the key for them to regain the ability to use nuclear weapons again like they did on Junius Seven. My heart pounded as it went up to my chest and I could feel it too as I struggled to figure out how warn the PLANTs of an impending nuclear attack on them until I remembered getting Yzak's e-mail address and began to type a message to him. This would be the beginning of the end for the Earth Forces and their attempt to wipe out the Coordinators.