Disclaimer: I hereby declare that I do not in any way own the rights to the anime known as Mobile Suit Gundam SEED, or anything else that falls under the Gundam meta-series itself, this includes the story, plot, characters, and mecha. I only own what I have created for the purpose of this story including the story itself, characters, and mecha.

Mobile Suit Gundam SEED: Raising the Black Flag

An Alternative Universe Story, based on Mobile Suit Gundam SEED

Written by,

William R. Woods

Aka "Deathzealot"

Or, "Deathzealotzero"

With some ideas and support from,

Seth M. Klein

Aka "Persistent Dreamer"


The basic idea of this story is an interesting one for it utterly destroys the canon storyline and plot of the series and rebuilds a whole new storyline around the remains of the original. This is of course completely different from several other Gundam SEED AU Stories which stick with the original plot or storyline and only do a few changes like adding a single original character or two and their mobile suits to the crew of the Archangel. While other stories there are a few minor changes done to the storyline like introducing a whole new group or faction to the story like my story Angelic Dawn. Or there are the stories which change the canon storyline halfway through their story. However not very many changes the entire storyline of the series, and even then only a handful of those do what I am going to do with this story redoing the whole story of the series. Oh! Not the complete story for the events of Heliopolis are still the same, a little, but it's everything else after the collapse of the colony that has been changed.

That said I bet many are wondering why am I doing this? Well, I am getting quite tired of all the AU SEED stories out there that are still loyally following the plot of the original series and only adding a few extras here and there. I figured why not go all out and rewrite the Gundam SEED story a bit different from the series itself. I know many would be upset by this for it may change the entire feeling of the series if I completely rewrite the story into something completely different. However I am not completely rewriting the whole story for some events will still happen including, Invasion of Orb (whistles innocently), Saving Lacus in the Debris Belt, Meeting up with Cagalli in the African Community, and several major events of the story will remain in the story. If I did so yes then this story wouldn't be SEED anymore in my humble opinion. That said other events are completely going to be changed or removed like the Artemis Fortress Arc has been modified drastically, the Triple Ship Alliance is going to replace entirely, etc. stuff that I and others usually do anyways.

However with all that said I haven't even mentioned the single idea of this entire SEED rewrite like I usually try to say in my forewords, so I don't get flamed in reviews about it later on in the story. For this story, this idea is actual that the Archangel going rogue and becoming of a sort-of pirate after a series of events early in the series convinces the crew to leave Alliance service. This is, of course, the reason behind the story's title which I am sure now makes some sense in the scheme of things. I must say though other than that I am not saying anymore and keeping the rest close to my chest no reason to reveal anything further than that.

Alright, I do believe that is about it for this Foreword. It is time to get to the story. So please I hope you all enjoy this new SEED story from yours truly. Ja ne!

William R. Woods

November 1, 2014

Prelude: Divergence

The Battle of Heliopolis is often said to be the first real turning point of the Bloody Valentine War where the Earth Alliance started to gain ground against the superior forces of the ZAFT organization. It would be the first battle of the war that had not only ZAFT but the Earth Alliance sporting mobile suits. While earlier battles had the Earth Alliance sporting mercenary operated mobile suits fighting for them, this action was the first to have an official Earth Alliance designed and built a mobile suit to take part in the fight. Therefore it was the turning point of the entire war

- Taken from The Genetic Issue: The Bloody Valentine Wars


ZS Vesalius
Heliopolis Nearspace
Lagrange Three, Earth Sphere

On the bridge of the ZAFT Nazca Class Destroyer Vesalius,the ship's officers were gathered around the tactical map at the back of the bridge getting ready to plan for what they should do next. The ship's commander Rau Le Creuset was frowning as he looked down at the map table before looking around at the others gathered around the map table along with him. On the map, a monitor showed the last seconds of the colony as it collapsed making the others frown as they watched as the colony became a large debris field.

"Commander the Council won't look lightly on the destruction of neutral nation's colony like this," the ship's captain Fredrick Ades mentioned a frown as he looked over at this commander seeing him with a small smile on his face.

"Captain Ades how can we call a colony producing new weapons for the Earth Alliance 'neutral' and besides the residents managed to make to the lifeboats, therefore, we should have no problems," the man replied with a nod of his head before floating away from the map table and over to the shoulder of the ship's sensor officer.

"Can you detect the enemy's new warship?" the Commander asked the man making the younger man stutter a bit before turning to his station to look through the readings the ship's sensors have taken in last few seconds. Captain Ades floated over to his command chair as he shook his head wondering why the man still wanted to go on after that ship.

"No sir not through all of this interference from the Colony Collapse," the officer reported a few moments later making the Commander nod in understanding before he looked out the bridge's viewport with a small thoughtful frown on his face.

"You still want to go after them, sir. We don't have any more mobile suits," Captain Ades mentioned as he watched the Commander move away from the sensor station with that same thoughtful frown on his face before he turned to look at the Captain at his comment.

"What do you mean Ades we have the four we took from the Alliance. The data extraction from them is complete after all. Besides I want to see what shall happen with two machines created by the Earth Forces do battle," the Commander mentioned with a small pleased nod of his head making the Captain blink in surprise at this before sighing for it sounded like something his commander would do after all. However, before he could respond to his commander, the sensor officer called out in surprise drawing the attention of the two senior officers to him.

"Three Heat Sources Detected! Red 15 by Orange 10," the sensor officer reported making the two officers look at one another in surprise at this before the Captain leaned forward.

"Do we know what they are crewmen?" Captain Ades asked the younger man who was frowning as he entered a few commands into his station before a beep came from the station as a pair of ship schematics appeared on his screen.

"Yes, sir, two Drake Class Missile Frigates and a single…Salamis Class Cruiser Carrier leading them!" the man reported making more than one crewmember hiss in shock at this. For the Salamis,Class was quite a boogeyman to ZAFT ships thanks to them commonly carrying mercenary operated mobile suits into battle. Not to mention more than one of these crewmen had been onboard the Laurasia Class Frigate Galvani which had faced off against a Salamis Class before during the Battle of Nova several months before. The Commander frowned at this as he looked over the shoulder of the sensor officer while he remaindered the same event and sighed as he leaned back.

"Sir we cannot hope to take on a Salamis Class like this with four untested mobile suits and pilots inexperienced in their operation," the Captain mentioned hoping the man wouldn't order them to attack those ships. However, he didn't need to worry. For the Commander knew that while he could have his forces hound that single new warship and its sole mobile suit even with the untested mobile suits, fighting against an Earth Alliance Taskforce that included a Salamis Class ship which could carry several mobile suits themselves with experienced veteran pilots is another matter entirely.

"No worries Captain I understand quite well that we cannot take those ships on without any extra support. Therefore contact the Gamow we are leaving and heading back to the Homeland," the Commander mentioned with an internal curse for he wanted to see the performance of these new mobile suits after all but he couldn't just throw away his forces like this. The Captain sighed in relief noticing a few of his crew doing the same at the corner of his eye.

"Yes sir," the Captain replied before relaying those orders to the communication and helm officers while the Commander floated off towards the back of the bridge once more.

"I shall be in my quarters, Captain. Let me know when we have left Lagrange Three," the man mentioned before departing the bridge behind not waiting for a response. Outside of the bridge's main hatch, the Commander could only curse to himself at this wasted opportunity. As the two ships of his team stopped before with side thrusters firing turned their bows away from the debris field of the destroyed colony and back towards the distant lights that were the PLANT Colonies of their homeland before their main engines lit off pushing them off away from the debris field. It looked like the Earth Alliance won this round, but there would be other chances on going after that new warship after all. However unknown to Commander Le Creuset and his crews this would be quite a long time before they would do so.


Post Chapter Notes

Well here is the Prelude and while some stuff has changed it is not the promised boulder thrown into the story, which will be the next chapter. That said this chapter shows what is happening with the Le Creuset Team, and it shall be the only ZAFT POV for a while though I am going to try to do a few ZAFT bits in the story if not in the story then official side stories used as Omakes at the end of some chapters.

There is nothing here that is special or anything but still an interesting turn of events that opens the story up. The Salamis Class and is background shall be actually revealed in the next chapter for it is kind of interesting in my opinion. Also, the Galvani is revealed to be Le Creuset's ship during the early battles of the war during one of the games and its side missions. I don't remember which one but an interesting idea that I thought to include in the story. The Laurasia Class page on the Gundam Wiki has an interesting image that features the ship in its image gallery.

That said I hope you all enjoyed this small tidbit, and I shall get the first chapter up as soon as possible. Thank you for reading this story, and I shall see you all in the official first chapter when I post it in a bit.