Ok I don't own Gundam Seed and this is a little confusing at first it is set in the Destiny half of Gundam Seed but there are key differences one of them being that Mu La Flaga wasn't the only person believed dead at the battle of Yachin Doe another is that Mu never lost his memories or was a part of the Earth Alliance though he was in their hospital for a bit but that's all I'm telling you for now the rest you'll find out as the story continues oh and one more thing Cagalli is never forced to marry into another family but that will be explained in the story as well so I guess you could consider this AU

well it had been two years since the battle of Yachin doe and things were different, a sort of peace had come between earth and the plants but there was no official treaty and Orb was affected the most because of the fact that they had decided to stay neutral should another war happen even though they did make mobile suits to protect their neutrality as was their right. It was actually the two year anniversary and the entire Archangel crew was at Cagalli's mansion to remember the end of the war and Yzak, Dearka and Athrun were there as well and it was Athrun who noticed Cagalli was distant that night like she had been the previous anniversary

"hey you ok?"

"no Athrun I'm not ok"

"what's wrong?"

"it's just that I..."

"you miss him don't you"

she just nods in agreement unable to talk at the moment and that's when Murrue Ramius also walks over

"you know I also miss Mu all the time but the anniversaries are the worst"

"at least you didn't lose your brother after only just having found him"

(sighs) "I know but you know as well as I do that if there was any way of his surviving Lacus or I would've found both him and Mu"

Athrun speaks up again

"and lets not forget Mr. Waltfield didn't stop looking until earlier this year even though he'd been ordered to stop much earlier"

well they rejoin the rest of the group and everyone talks about their memories of either the exceptional pilot they had or Mu. Three weeks later the war started up again and Cagalli literally had to flee her homeland because Earth Alliance had force ably taken over it but they got a shock in the battle to let Cagalli escape, because Athrun hadn't trusted Jibril from the start so he hadn't rejoined ZAFT instead he was part of Orb's army he was there too, they heard a voice they didn't think they would ever hear again and actually Andrew Waltfield also got a shock

"get the princess out of here Murrue, we've got your back"

(quietly) "Mu?"

suddenly someone else speaks up

"talk later and fight now La Flaga or have you forgotten your own protocols when going into battle"

this time it's Waltfield who's in shock but Mu La Flaga preempts it by being the voice of reason

"valid point missy, listen Archangel get the princess to safety, we'll talk once that's done, coordinates are old Josh-A that place was abandoned when the cyclops bomb went off and they never came back partly because of us"

(snort) "what do you mean partly La Flaga we beat them back enough times to let us keep the land and you know it"

"true but I wonder what they would say to me being the one to leading the rag tag group that has that place seeing as how I'm technically a traitor"

suddenly Cagalli speaks up interrupting the little conversation between La Flaga and the mysterious person

"hate to break it up you two but we're in trouble here"

"on it"

and so with a little skill and luck they manage to get the Archangel to safety and also got the mysterious group with them as well and well Andrew Waltfield fainted in shock when he saw that it was who he thought it was but then again no one could blame either him or Captain Ramius who also fainted. Three hours later the two of them were conscious again

"Mu tell me I'm not dreaming"

"you aren't"

suddenly Waltfield asked the same question only slightly different

"Aisha is it really you?"

"yes Andrew it's me"

"but how?"

"that's an interesting story and well, let's just say you won't be too happy about it at places, but first can you get the princess in here it's important she's in on this conversation"

And so Cagalli is with the rest and Mu La Flaga explains how he's alive after two long years

"well two years ago when I woke up I realized that I was in an Earth Alliance hospital unable to practically do anything useful so for the next month I pushed myself in the rigerous physical therapy they gave me and I gave myself and once I could sort of walk I made my escape knowing that they would erase my memories like they did another person who I didn't see until I went back after my escape and getting a group, well anyways I made my escape and even though I knew the best place for me was Orb I didn't want to risk the crew if they were still alive so I thought of one other place that had for sure been abandoned still and wouldn't get me captured again I went to Josh-A and that's where I found Aisha with a rag tag group of people thought dead but actually still alive"

"as for me I'm not entirely sure how I survived the explosion but I woke up in an entirely different place and without Andy so I had to initially presume he was dead and also made my way to Josh-A about a half year before La Flaga. When he arrived I was initially nervous even though he was wearing civilian clothes, which he bought with what little money he had on him at the time of his escape, because I recognized him as the Hawk of Endimion"

"let's just say that it took a few days in a holding cell and long talks for her to at least release me if not fully believe my story that I was no longer an Alliance soldier, had joined forces with the destroyed nation of Orb, and was currently considered dead and that hopefully the war was over with and that Orb and the Archangel had won"

"well I actually had a spy in Orb, he's still alive as far as I know, and sent a coded message to him to find out the truth and within days I got his return message that everything La Flaga had said was true after Josh-A the Archangel had indeed left the Alliance and joined Orb and I also found out he was considered dead after the last battle along with someone else and that the war was indeed over and I actually trusted him enough to make him leader of our little group"

"not after completely gaining the trust of the others but after they noticed Aisha trusted me they slowly trusted me as well which was a good thing considering what I planned a year after I had escaped from the Alliance hospital"

"by this time he could actually walk properly again without a limp in his left leg which for some reason took longer to heal then his right"

"don't ask me well anyways so we went back to the facility I escaped from and then I found him...I found the kid with his memories completely wiped from the Alliance scientists doing and I couldn't convince him that his name was Kira Yamato and not Neo Roanoke so we fought in hand to hand and he actually managed to injure me again but thanks to our plan Aisha got to me in time and saved me and we escaped back to Josh-A which was ours after several skirmishes with the Alliance who just wanted the place back to rebuild probably but I hope that they figured that some locals from a far distance away just wanted to settle there and get away from society so they sent a general message saying we could keep the stupid place if our freedom from society meant so much but never ever touch the military stuff because we might accidentally set something off killing ourselves and quite possible others in the process, naturally we didn't listen to that half of the message because of who we were"

" and so we built the suits you see before you with an OS system designed so I could handle any one of the machines in case of an emergency and we've been fighting Kira trying to get his memories back ever since"

"so Kira's alive, my brother survived Yachin Doe like you somehow did?"

"whoa back up brother?"

"yes" (sighs) "it turns out that they were separated at birth Kira found out through Cagalli but they've never had the chance to get to know each other outside of battle"

"whoa so how do you feel about protecting your brother's sister Athrun?"

"I feel honored to be doing so"

"Aisha I have to ask, has being separated from me been as painful as..."

"I'm sure it was Andy and when I found out you were alive and part of the Clyne faction I knew you were following your heart and that I would have joined you in an instant if I was there having started to doubt ZAFT after I woke up essentially abandoned"

"look for now we need to think about what to do next and also think about how to get the kid to regain his memories"

suddenly one of the members of Mu's and Aisha's group showed up

"sir we have a problem"

(groans) "since when do we not lately, what is it?"

"our base has been destroyed by the Earth Alliance in their message it says and I qoute 'you no longer deserve this abandoned base having used it to help the traitorous Orb union' end qoute and we had fifty good men still there too"

(gasps) "the support unit, but I thought they were supposed to leave yesterday"

"they were so unless something happened to delay them the Earth Alliance is lying to us about their deaths"

"so you were already planning on abandoning Josh-A?"

"actually part of that is that we didn't trust the alliance to keep it's word past another war so we were always ready to join the Orb union should another war break out"

"and the other part Mu?"

Aisha steps in laughing with good reason

"it's simple we simply no longer had the room to keep everyone alive and happy, you see shortly after La Flaga here showed up we split the group into two sections the warrior section which La Flaga and I are part of and the refugee section in which we give refuge to tons of civilians who don't want to fight but also have no other place to go"

"but do they like living with soldiers?"

(sighs) "it's not the best arrangement unfortunately, the civilians and soldiers occasionally clash and that's when I have to step in as head of the entire camp but we make due with the situation as best we can"

"the only real time we've had problems is when we've been fighting for days on end and the civilians are getting tired of being in the safety bunkers and the soldiers are just plain tired because of the constant fighting that goes on"

Andrew steps in

"basically what you're saying is that when there's fighting going on people are on a short fuse and can blow up any second"

"exactly and what's worse is that some of the refugees have learned about one of the enemies being Kira, a coordinator and the ultimate one at that, the one who defied everyone to follow his own path"

"how did they find that out?"

"don't ask me because I have no clue I've only ever talked about the kid to Aisha and that was always in the privacy of the office"

"well for now we have to think about freeing Orb from the Earth Alliance since they will no longer be neutral"

"and getting Kira back with us is also going to be a top priority"

and so they finally get Kira back on the ship but it just wasn't working even when Lacus came on board it wasn't working but suddenly he was on the bridge for the battle of Orb and he heard Cagalli claiming her title as leader of her nation in the Akatsuki and the fierceness of her voice is what brought him back to them

"what's my sister doing out their in a mobile suit?"

"Kira is it really you?"

"yes commander it's really me"

"great you have your memories back"

"yes I do now then can I have an answer to my question?"

"the only thing I know is that Lord Uzumi left something for her and she was taken to it when she declared she wouldn't let her country burn again"

and so they free Orb, go into space and ultimately defeat jibril and peace was established for a long time unfortunately it would always be a tense peace even with the kids of heroes growing up and eventually they would be forced to fight in another war, once that would be much worse than their parents ever fought and also without the guidance of their parents because they were killed right before they joined the Orb alliance military...or were they dead? Only time would tell