Pinned A/N: Hello. This is my first time posting here. I have written a lot of Fanfiction (mostly about Gundam) but I have never published it here before. I am a big fan of the Gundam Series and thus I am writing either altered versions of their story or originals based on existing material. There's just this thing about my writing: I always write in plot format. So please forgive me if you don't like this format or if the story becomes confusing.

Pinned A/N #2: Everything that happened in Gundam Seed (Remastered) stays exactly the same. Meer Campbell doesn't exist in this story. Nothing personal, I just thought that the overall story would still work without her.

A/N: This chapter may not look like it has any major changes but most of the changes have to do with character's motivations and reasons. Also I think that the ZGMF-X23S Saviour had a lot of missed potential so I retconned its destruction and brought it back as the Saviour Repair (just think of the Exia R1 and apply it to the Saviour). Also I didn't want Athrun just sitting around doing nothing when the Saviour was destroyed.

GSD II – The Certain Uncertainties

Shinn and Rey discover an abandoned Extended facility of the EF. Rey reacts negatively and is brought back to the Minerva. Talia and Arthur make a thorough investigation and discover a lot of info about the Extended program.

The Phantom Pain hears about the infiltration, and Auel goes paranoid thinking his mom would die if ZAFT keeps poking around. Sting tries calm him down but Stella heads off to the facility in the Gaia after hearing her block word.

The Saviour and Force Impulse intercept and disable the Gaia. Shinn discovered that Stella is the pilot; he immediately brings her to the medical bay of the Minerva. This obviously confuses everyone. Rey reported the incident to the higher ups, Soon enough, Captain Gladys receives word from the council that they want a living extended brought to them for examination ASAP. So they decide to head out after resupply and repair.

They head out and the largest EF and Orb force ambush them. They fight desperately but the Freedom and Archangel appear once again and attacks everyone on the battlefield. Cagalli also heads out and tries to stop the Orb forces in the area to stop attacking the Minerva and go back to the mainland.

Her words do nothing but anger Shinn, causing him to fire eight missiles at her. The Freedom uses its Picus to shoot down all missiles. It charges at the Blast Impulse but the Saviour intercepts it before the Freedom can get close.

The EF and Orb force resume their attack on the Minerva and the Archangel. Captain Gladys declares the Archangel their enemy. The Murasames charge at the Minerva but Cagalli uses the Strike Rouge to block their path. She learns that the Sarans now rule Orb (and in turn, are puppets of the EF). Baba's Murasame throws the Strike Rouge out of the way and resumes their charge on the Minerva.

Lunamaria and Rey desperately tried to defend their ship but they couldn't stop the barrage of missiles and machinegun fire. Lunamaria's Gunner ZAKU was totaled, injuring her.

Shinn destroys the Abyss and kills Auel. Athrun once again tries to talk Kira into stopping. Kira ignores him, disables the Chaos, and engages the Blast Impulse. Shinn suddenly remembers the Freedom from two years ago and attacks it angrily. Even though he was a match for the Freedom, he was ordered by Athrun to return and help the Minerva because Lunamaria got injured and her ZAKU is out of action.

Shinn switches to the Force silhouette. Baba and his squad go for one last kamikaze charge on the Minerva. The Force Impulse was able to shoot down all Murasames except for Baba's, who successfully rams his Murasame on the Minerva, inflicting heavy damage on its bow (and also damaging Rey's Blaze ZAKU Phantom).

Shinn switches to the Sword silhouette and destroys numerous mobile suits, warships, and carriers from both EF and Orb. Cagalli tries to stop him but is no match for Shinn. A squad of loyal Orb soldiers forced Cagalli to retreat.

The Takemekazuchi charges the Minerva. The Minerva was still able to inflict crippling damage to the carrier. The crew (and Jona) of the Takemekazuchi abandon ship and [those who are still loyal to Cagalli] head to the Archangel as per Colonel Todaka's orders.

Kira and Athrun battle it out because he thinks that Kira is endangering Cagalli by putting her in the front lines (among other things) but Kira tells him that Cagalli is really trying her damn best to stop Orb from participating in the war. The two argue and fight a little bit more but the Freedom ultimately defeats the Saviour. Shinn destroys the Takemekazuchi, killing Colonel Todaka.

Lacus tells Kira that she wants to go to the PLANTs to gather more information about Durandal. Kira objects but Lacus convinces him to let her go. Lacus and Waltfeld disguise themselves and snuck past ZAFT soldiers and checkpoints in an airport. They are found out and the Captain of the military police order his men to shoot down the shuttle Lacus was on.

Several mobile suits shoot the shuttle but before they can hit it, the Freedom enters the scene and disables all the mobile suits in the area. Kira contemplates on whether he needs to go with Lacus. She tells him to stay with the Archangel. Waltfeld promises Kira that he will protect Lacus with his life. Kira asserts that Lacus needs to be careful but before they could say anything else, the communication was cut. Lacus successfully escapes.

Durandal hears about Lacus' stunt and he realizes that she's up to something. He tasks Special Forces to follow her and if need be, eliminate her.

The Minerva goes back to the base at Crete for repairs. Stella's condition worsens and is at the brink of death. This caused Shinn to sneak her out [return her to Neo]. But before he can, Rey catches him. They talk a little and Rey decides to help Shinn. Rey hacks the gates and let's Shinn out in the Impulse. He contacts Neo; they meet and he gives Stella back. With the promise of keeping her away from war and fighting, they part ways.

Shinn returns and is thrown into a holding cell. Rey is also thrown in a cell for his participation. Athrun hears about what Shinn did, but decided not to say anything to the authorities. He talks to Shinn privately and tells him that he will side with him if worse comes to worse.

In Germany the EF deploys their new weapon, the Destroy. The pilot chosen for it was Stella. The Destroy, Chaos, and Neo's Windam wreak havoc in Germany. Shinn is cleared and released because of his achievements recently (and because he was the only ace pilot with a properly working Gundam). After hearing about the events in Germany the Minerva [is ordered to] and the Archangel [decides to] go there.

The Archangel arrives first and the Freedom engages the Destroy (they intercept it in Berlin). Cagalli, in the Strike Rouge, engages the Chaos and the Murusames engage the Windam. The Freedom can't seem to harm the Destroy. When the Minerva arrives, Shinn and Kira team up for a while. The Impulse destroys a portion of the cockpit hatch and sees that the pilot is Stella. He calmly approaches and the Destroy stops attacking. The Saviour Repair launches. Athrun teams up with Cagalli and together they defeat the Chaos. The Freedom shoots down the Windam. Kira tells Murrue to retrieve the fallen pilot.

This causes Stella to panic and start attacking again. Kira then tries to attack the Destroy but instead, Shinn attacked him. Cagalli and Athrun tried to damage or at least distract the Destroy. The Strike Rouge and the Saviour Repair then come up from behind and destroy its main battery pack, causing the Destroy to slowly lose power. The Impulse and Freedom battle it out, and as the Freedom was about to stab the Impulse dangerously close to the cockpit, Stella uses the last bit of the Destroy's backup power to shove the Impulse away and use the huge mobile suit as a shield. The Freedom instead stabs the chest cannons of the Destroy. Stella saves Shinn but she gets caught in a fatal explosion. The Archangel and crew then retreat as ZAFT reinforcements arrive.

Shinn holds a dying Stella in his arms and she kisses him after declaring her love for him and dies shortly after. This causes Shinn to hold a grudge against the Freedom (and its pilot).

Chairman Durandal uses the Berlin incident as a reason to declare the LOGOS as the true enemy of mankind. The Archangel is also labeled as a target and the ZAFT Eurasian force was sent to sink it. Minerva is also ordered to participate in the Operation (Operation Falling Angel). Shinn, in a rage fueled motivation, has studied and analyzed the Freedom's fighting pattern. Athrun refuses to participate in the mission.

Shinn uses the Impulse's block system to gain a significant advantage over the Freedom. Not only does he isolate the Freedom, he also prevents it from helping the Archangel. The ZAFT Eurasian force use overwhelming numbers to slowly but surely surround and pressure the Archangel. The Force Impulse is able to significantly damage the Freedom, forcing Kira to retreat.

As the Archangel approaches the sea, the Minerva fires its positron cannon at the Archangel in hopes of sinking it before it can dive. The Force Impulse impales a retreating Freedom below the cockpit (closer to its waist) allowing Kira to survive. There was no nuclear explosion. The Freedom exploded normally because Kira cut off the power of the Freedom at the last second. Shinn wonders of he did the right thing, and if what he did really avenged Stella.

Back in the Minerva, Shinn goes straight to his room and contemplates. An angry Athrun follows him and talks with him privately. Shinn reveals that he knew he missed the Freedom's cockpit and that the pilot may have survived. He explains that he got brief glimpse of Stella before he impaled the Freedom. Athrun is pleased to hear this but his doubts about ZAFT increases. He tries to emotionally support Shinn in his troubled state.

Kira awakens and talks to Neo (thinking that he is Mu la Flaga) but Neo assures him that he is not the man Kira thinks he is. Murrue suddenly enters and asks Kira if he is alright completely ignoring Neo. But Neo asks about Mu, making Murrue run away, crying.

The Minerva arrives at Gibraltar and Chairman Durandal requests to meet with Shinn and Athrun. He shows them latest machines from ZAFT; the ZGMF-X42S Destiny and the ZGMF-X666S Legend. Athrun is displeased with the offer while Shinn accepts the Destiny. After showing the Destiny and Legend to them, Athrun decides to go back to his room and think.

Chairman Durandal meets with Rey and asks him about what he thinks of Athrun. He tells him that he [Athrun] is a threat to the plan and must be eliminated. Durandal agrees, and plans to charge him with a crime (treason; thanks to Lunamaria's spying) and have Rey take care of the rest. Shinn overhears this and immediately goes to Athrun's room to tell him about it.

Athrun realizes that Durandal has no more need of him and decides to run away. He tries to take Shinn with him but he refused. Saying that there may still be a chance to change his [Durandal] mind. Athrun sternly tells him that that is not possible; that the Chairman is very manipulative and one day, will have no more need of him [Shinn], and eventually kill him. He also asks how he plans to run away and he said he'll think of something.

After a few minutes, the guards knocked on the door demanding Athrun. Athrun then punches Shinn, breaks the window, and apparently escapes. The guards enter and find Shinn on the ground saying that he tried to stop him but got knocked to the ground. As one of the guards look out the window, Athrun knocks him, and the other guards out. Shinn then tells him to stick to the plan and they go their separate ways.

Athrun then ends up in Meyrin's room. Lunamaria and other guards knock at her door, she [Meyrin] covers for him by answering the door, pretending that she just came from the shower. Lunamaria gives her some time to dress up and she closes the door. Athrun asks why she helped him she responds with "I don't know". As he was about to leave, Meyrin stops him and decides to help him more. She hacks the computer and sets off an alarm by the Bay (the other side of the base) luring the pursuers there.

They escape using her car, but Rey sees Meyrin and gets suspicious. They arrive at the hangar and decide to board the Saviour Repair. Rey then pops out, starts shooting and declares them both traitors. Athrun tries to convince Rey to let Meyrin go but to no avail. Athrun shoots Rey's gun, causing him to drop it, and the two used the opportunity to board the Saviour Repair.

Rey contacts Shinn about Athrun escaping. Durandal orders them to pursue. Rey informs Durandal about Meyrin's choice to go with Athrun and they get the all clear to shoot them down. Shinn is surprised that Meyrin is with Athrun. They confront each other and Shinn "tries to talk him into surrendering" but Athrun flat-out refuses. Rey tells Shinn to kill them because even Meyrin has become an accomplice to Athrun's crimes. Shinn begins to realize the truth to Athrun's words. The Destiny impales the Saviour Repair; purposely missing the cockpit. It [Saviour Repair] falls to the sea and explodes. Rey didn't notice Shinn missing the cockpit and just presumed that they both died. The two return to base.

A/N #2: Honestly, can this plot be turned into a 2 hour movie? Just a random thought. Also, I know there are a lot of brackets here; I just want it to be less confusing as possible.

A/N #3: I promise there will be major changes in the next chapter.