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 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"

Phase Five: Madorna

The organization known as Madorna Workshop started as an independent group of engineers who customize both mobile suits and ships for the right price. This allowed independent mercenary pilots to customize their mobile suits far easily then if they did it by themselves. The group has since become a notable producer of their own mobile suit line with the introduction of the MWS-001A Boral Worker Mobile Suit and its variants including the combat-rated MWS-001D Boral Defender and MWS-001G Boral Guardian variants. They also sport their own GINN variant they make out of exported GINNs from the PLANTs, the MWS-1017M GINN Marauder which is different from the custom variants they do at the request of a customer. Overall they are set to become the Third Party Mobile Suit Developer in the coming months with rumors stating they are looking to produce a true original combat-rated mobile suit instead of a variant of another mobile suit...

- Taken from The Third Path: The Neutral and The Third Parties of the Earth Sphere

-o-o-o-

Observation Room
Main Docking Bay 3
Hephaestus Station

In a large observation room that looked over one of the space stations large docking bays a trio of figures watched as the rouge Atlantic Federation warship Archangel docked in the mentioned bay. The trio of figures where quite different with the first being a tall, skinny man with a pair of darkened glasses covering his eyes and long white hair done in a ponytail down his back. He wore a rumbled pair of engineer coveralls that had a coat thrown over the top which sported an emblem on its back. He was staring down at the ship with an impassive face that was partly covered by his glasses and his arms crossed over his chest. The second is a woman who was leaning against the first man and sported long purple hair done in similar style to the man and wore a nice two-piece suit. She was looking down at the ship with a small pleased looking smile, one that a mother had when a son or daughter returned home. The last figure is a short Hispanic looking man who sported a bristling black mustache as he glared down at the ship with black beady eyes and one hand ruffling his short, crazy salt and pepper hair.

"So this is the ship that had been the catalyst leading to the destruction of Heliopolis Colony?" the first man mentioned as the docking clamps locked onto the ship bellow them. He was surprised by the shoulder slap from the woman at his side.

"Be nice Max! It wasn't their fault that Heliopolis was destroyed and everything that has happened since then," the woman mentioned to the man one Maxton Madorna, the overall man in charge of Madorna Workshop and Hephaestus Station itself.

"That is true Pearl," he replied with a sigh to the woman, his own wife Pearl Madorna, who nodded at this before turning her attention back to watching the ship bellow them before the snarl of anger from the second man surprised the two of them.

"Gah! I cannot believe this! Those damn bastards used my G-Class Plans without asking me about using them," the man angrily stated with another angry snarl as he glared down at the ship bellow them. Pearl only sighed at this before making her way over to the man's side.

"Calm down Jose. Yes they did use your plans as a base for this ship but do you blame them for you had been working for the Atlantic Federation at the time after all," she mentioned to the man one Jose Weaver, a notable naval engineer and ship architect who had a large hand in designing many of the current space warships in use by the Earth Alliance. The man only looked over at her for a moment before sighing and nodding his head at her.

"Yes that's true Pearl but that isn't the only thing I am angry about this for look at it," he mentioned pointing down at the now docked ship.

"While they do use the G-Class design as a base they basically perverted the design into something else entirely," he continued on with another angry snarl before calming down once more at the look from Pearl who only sighed before looking over her husband to see him nodding in some agreement with the other man.

"Alright listen to me you two for this could be good for us if we play our cards right, for think about it for the ship did go rouge for some reason or another. They choose to come here for alyssum therefore Jose you can fix this perverted version of your design. Max did you forget that this the ship had been part of the Earth Alliance's G-Project therefore it is bound to have the data needed for you to complete your new mobile suit design," she said to the two men who blinked at her in surprise before looking at one another before starting to smile for she is quite correct.

"That is right I had forgotten the Archangel was the ship designed to carry the Earth Alliance's G-Weapons. Thank you my dear," Max replied with a nod of his head towards her before turning back to look at the Archangel bellow them with a more thoughtful look on his face.

"Yes Pearl thank you for this maybe the chance to show up this bastards at the Atlantic Federation Advanced Research and Development Department," Jose mentioned with almost giddy look on his face making Pearl shake her head in both amusement and some embarrassment at the man for he was almost a kid sometimes.

"Yes I believe I am going to go to my lab to see what I can do with this," the man mentioned before getting ready to run over to his lab before stopping and looking over at the figure of Max.

"Oh, send me any data on the ship you can get Max?" he asked making the other man only wave his hand in answer before Jose nodded himself before finally rushing off. Pearl only sighed at this before turning her attention to her husband.

"Alright husband of mine let's go down to the meeting room so we can meet with them when Flit finishes his little tour you wanted them to be taken on," she said grabbing his arm making him blink down at her before nodding in agreement.

"Yes let's go then my dear," he replied before letting the woman lead him out of the room and towards one of the large meeting rooms.

-o-o-o-

Causeway
Main Docking Bay Three
Hephaestus Station

With the Archangel docked safely with the Station the ship's officers disembarked from the ship with Flit in the lead. The officers where a little surprised that no one was waiting for them on the causeway leading to the main hatch. The small group quickly made their way through the dock section and saw that the other two docks in this section of the docking bay where occupied as well, though not one they recognized, though it did seem somewhat familiar to the former Atlantic Federation officers. Captain Ramius turned to their guide to ask the man what ships those happened to be.

"I'm sorry Captain but I am not at liberty to say currently for until you are officially offered asylum here at the Station you are only guests therefore some information is of course not for you to know. Not to mention it is not our choice for you to know anything about those ships," Flit mentioned with a frown nodding to the two ships making Captain Ramius sigh before nodding in understanding while Ensign Badergueril was still straight faced but she did blink a bit at this and Lieutenant La Flagga only shrugged knowing that they may be told later on.

"However Captain while I was told not to reveal anything about these ships I was told to take you the long route to the meeting room basically showing off some stuff about the station. Please remember some questions may not be answered till you have the chance to meet with the Chief," Flit mentioned when they left the dock section behind and started towards the main factory section of the station. The three officers could only nod in understanding at this before being lead through numerous areas of the station including what looked to be a complete factory line for mobile suits much to their amazement while Mu only looked on with a small smile on his face. Finally Flit lead the three of them into another part of the station making both the Captain and her XO gasp in surprise as they found themselves on a catwalk suspended over a large hangar like room while Lieutenant La Flagga who had seen this before only chuckled before looking over at the hangar. It was quite busy with numerous people rushing around putting final touches on several brand new MWS-001G Boral Guardian mobile suits while a few of the regular MWS-001A Borals where undergoing what seemed to be general maintenance of some sort. However what really attracted their attention were three brown colored mobile suits that took up one corner of the hanger which had the most people surrounding them along with various pieces of equipment attached to them.

"The MWS-002 Combat Mobile Suit Prototypes," Flit answered their unasked question with a deep frown staring down at the three mobile suits. The three officers only stared down at them as well before turning to look at the man.

"I take you have been having problems with them Flit?" Mu asked the other man which caused the man to sigh before turning attention his attention to the younger man and the other two officers.

"Correct Mu for while we have ironed out many of the general bugs out of the design one thing keeps tripping us up," he answered with a shake of his head eying the mobile suits once more.

"Let me guess the Operating System?" Captain Ramius asked with a sigh of her own looking down at the three mobile suit prototypes. Flit blinked at this before looking over at her chuckling a bit.

"Yes and No Captain for we haven't come up with a true Natural Use Operating System we do have access to an AI Driven Operating System which we finally managed to iron out any of the bugs in the design and started to introduce mobile suits with it," he explained waving at the brand new Boral Guardians spread out throughout the hangar.

"However while we did manage to work out the bugs with it there are still a few problems with it which I am sure you are aware of since Mu here had been piloting that mobile suit of yours when we first met up," he said continuing on making the three officers nod in understanding but kept silent on the man assuming that Mu was using an AI-Driven OS instead of a new Natural Operating System. Flit didn't notice the glances between the three officers and was looking down once more at the prototype mobile suits with a deep frown on his face.

"No the real problem we have with these prototypes that we wanted a mobile suit that can be not only piloted by everyone but a superior machine over the basic GINN since we already have the Boral Guardian and GINN Marauders which are on the level of the GINN. We wanted to go further than that with this mobile suit design but are running short currently," Flit said finishing his explanation making the three look at one another again with Lieutenant La Flagga looking between Flit and the others with an inquisitive look on his face. The Captain sighed before nodding to the puppy dog look of Lieutenant La Flagga who grinned at her nod before turning his attention to Flit.

"Well then Flit you guys are in luck for we have everything from the Atlantic Federation's G-Project stored onboard the ship even some stuff from their so-called Second Phase. With all that Data I am sure you can finally finish the design like how you want it," he mentioned with a large grin on his face making the older man blink at him in surprise before smiling in pleasure at this offer before looking down at the prototype mobile suits trying imagine them complete with the data from the G-Project. However Mu wasn't done for he retrieved a small disk from a pocket and waved it in front of Flit's face making the man look over at Mu with a raised eyebrow.

"And that isn't all Old Man. For we also manage to liberate a prototype Natural-Use Operating System from the Atlantic Federation before we went rouge. We then streamlined it and is the same system I was using to pilot the Strike earlier" Mu explained to the now shocked man who eyed the disk in front of his face.

"This will make the Chief very happy to hear this," Flit mentioned with a large smile splitting across his face. Mu only chuckle at this before looking over at the Captain with a victorious expression on his face making the woman only sigh and roll her eyes at the man.

"Alright then Old Man let's not waste any more time and meet with the other Old Man," Mu mentioned turning away from the view of the hanger and nodding towards a distant hatch leading further into the station. Flit only glared over at the younger man before sighing and exchanging a look with the Captain who only shrugged with small smile on her face.

"Yes let's get going before I smack you across the back of the head like you deserve," Flit mentioned with another glare towards the younger man who only smiled sweetly in response making Flit sigh and start moving towards the hatch leading to the rest of the station.

-o-o-o-

Main Briefing Room
Hephaestus Station

In one of the larger briefing rooms a door opened and Flit lead the three officers of the Archangel into the room. Already in the room where the forms of Maxton and Pearl Madorna along with a couple other men. One in a nice two-piece business suit and the other in a set of fatigues both of which were glaring over at the three former Atlantic Federation officers. Flit didn't even flinch at the appearance of the two extra persons in the room and quickly walked over to the front of the large briefing room table.

"Chief Madorna I like to introduce you Captain Murrue Ramius, Ensign Natarle Badgiruel, and this young scamp who doesn't really need an introduction," Flit mentioned with a scowl at the end eying the younger pilot who only tried to look innocent but was failing due to the look from Pearl. With the introductions done Flit quickly excused himself and left the room behind not before shooting Mu a victorious smirk at the looks he was getting from his pseudo-parents.

"Hi Uncle Max and Aunt Pearl," Mu said with a sheepish looking expression making the two Madornas to only look at him with raised eyebrows.

"Unbelievable," Max mentioned with a shake of his head eying the younger man who considered to be another son who continued to look a bit sheepish and trying to find a place to hide from the looks from the two people that had practically raised him were giving him.

"Kid you sure wanted to make a splash on your homecoming," Max mentioned with a small smile on his face making Pearl nod in agreement with her husband. Mu only shrugged at the looks before looking over at the amused looks on his companion's faces making him scowl a bit. Max then noticed the looks from the other gentlemen at the table before sighing and leaning forward putting his hands underneath his chin.

"I do apologize Captain Ramius but we haven't seen our so-called second son in a long awhile therefore with that out of the way we should get to the main event," the man mentioned with a nod to Mu who noticing the serious expression on his pseudo-father's face quickly took a seat at the head of the table and sighed for this next hour or so is going to be quite painful.

"I agree Chief Madorna," Captain Ramius replied nodding to the man before eying the other two men at the table wondering who they are but if Max noticed he didn't mention anything instead leaning back in his seat.

"First of all there has been a few different versions of what happened at Heliopolis and I believe we shall see about getting the true story from someone who was actually there," Max mentioned making Murrue nod in agreement.

"Of course I would be happy to brief you on what happened at Heliopolis. We even brought our own records and readings from the start of the ZAFT attack and to when we left Lagrange Three," Murrue explained making Max nod with a smile not even looking at the surprised looks on the still unintroduced men at the table before leaning forward and tapped something in front of his position. A moment later a whine sounded as a screen was lowered behind the three officers and a small data-port popping up from the table in front of them making Murrue nod before turning and nodding to Natarle who retrieved a small data disk holder from a pocket.

"Very well the first bit is from a corrupted file we managed to retrieve from a remaining data drive found in the remains of Heliopolis," she mentioned with a nod towards Natarle who slid in the first data disk into the port. Murrue then for the next thirty minutes brought her audience from the start of the attack with a video showing the approach of the ZAFT ships towards the colony and all the way to the final collapse of the Colony. She then went right into the following incident between the Mycale, its taskforce, and the Archangel, along with the Strike. The destruction of the Lifepod found everyone at the table cursing in shock before Murrue continued on with the Strike's attack on the Mycale and its taskforce.

"After this we started salvaging operations finding no survivors from the Taskforce but finding a heavily damaged Earth Alliance GAT-00D Long Dagger Pre-Production Mobile Suit which we discovered a prototype Natural-Use Operating System in its computer," she mentioned winding up her presentation nodding to Mu who once again retrieved the disk containing the copy of the perfected operating system from his pocket and placed it on the table. This made Max blink in shock eying the disk making Mu smirk.

"During our salvage operation we managed to recover that damaged Lifepod that the Strike had recovered earlier and lost during the attack from the Mycale along with three more damaged pods which contained around four hundred refugees between them. Soon after we finished up our salvaging operation and started to head out of Lagrange Three heading towards here," she said finishing up her presentation. The four members of her audience could only shake their heads in shock at this story before one of the two unknown men angrily started to curse in another langue before the second man, the one in the business suit sighed and leaned back in his chair not even giving his companion a glance.

"D-Equipment! The report we managed to get from ZAFT didn't even mention anything about this," the man mentioned with an angry snarl on his face before sighing again and looking over at Murrue and her officers.

"I do apologize Captain Ramius for not introducing myself earlier for I wasn't sure what to believe what happened at Heliopolis. That said I am George Allster from Orb's Foreign Ministry and this is Lieutenant Colonel Hiroshi Soga of the Orb Space Defense Forces," the man mentioned with a nod to the still cursing man at his side before leaning forward with a smile on his face. Murrue only smiled in return and relaxed a bit. While Mu blinked in surprise for one of his pilot trainees is Flay Allster and briefly wondered if the two are related.

"Then that is good sir for like I mentioned I do have four hundred or so refugees onboard the ship that I believe would like to be returned to the mainland," she mentioned with a nod towards George Allster who only blinked in surprise at this before exchanging a surprised look with Pearl and Max before returning his attention to Murrue.

"Captain you don't know what happened?" he asked with a curious look on his face making Murrue look over at Mu and Natarle in confusion who looked just as confused as she happened to be.

"Know what Mister Allster?" she asked after a moment looking over the table at Max Madorna who sighed and leaned back in his chair rubbing his forehead in some disbelieve while his wife Pearl who had remained silent throughout the earlier presentation only leaned forward with a frown.

"Didn't you pick up any communication traffic during your trip here?" she asked making Murrue once again exchange looks with Mu and Natarle before looking over at the woman with yet another confused look on her face.

"No ma'am I ordered that we do a full Silent Run towards the debris belt, since we were worried about patrols from Artemis managing to intercept us. In fact we were stuck in a small debris cluster on the edge of the Lagrange Three area for two days to avoid such a patrol. The Silent Run also includes a Full EMCOM Procedure where we didn't receive or transmit anything during it," she explained to the woman starting to feel her stomach starting to fall for whatever had happened looked to be not good at all. George Allster sighed at this before exchanging a look with Max and looked over at them with an expression of pity.

"Captain I am sorry to tell you this but on January 30, the Earth Alliance invaded the Orb mainland taking control of the entire country," George mentioned with a sorrow-filled look on his face while the three former Earth Alliance officers could only stare at him in shock for this was the last thing they expected. Things had just gotten serious for the three for it was more than just a single colony destroyed and one of its civilian lifepods destroyed as well.

-o-End-o-

Post Chapter Notes

/whistles innocently/

I did say there was another large boulder that was going to be thrown into the story line and it looks like this is it folks. Yes Orb was invaded a lot sooner than canon in this story and I am sure there are going to be a lot of questions about this. No worries I am sure many are going to be answered in the next chapter.

That said we are introduced to Max Madorna and his wife Pearl which are of course based on Mukured Madorna and his own wife Laraparly. Also introduced is one of my main original characters Jose Weaver which is used in several of my stories and unlike in some other stories he is solely a Naval Architect in this story instead of having his fingers in many pies like my Diverging SEED Series. He also is a bit crazy in the head during this due some issues revealed later on. As for the G-Class Plans he mentioned well that is another thing that can be revealed in time.

A small change to the story is that George Allster is not the Vice Foreign Minister of the Atlantic Federation in this story instead sporting a similar position in the Orb Union. This changes Flay's character a bit and her story shall be revealed a bit later as well. The main reason behind this change is that I wanted to make Flay a mobile suit pilot for this story since I love the whole idea of her being a pilot. Therefore I had to change her character around a bit to make this work for her. Not to mention gives us a high-ranked civilian member of the Orb government to use as a sort-of leader for the Heliopolis refugees, at least till Cagalli is introduced later on.

I do believe that is it for these notes and time to get work on the next chapter before I get lynched for I do know you all are eagerly awaiting this chapter. That said see you folks then.