Well, this is a project I started to recreate Gundam Seed Destiny's ending, taking the first two thirds or so of the series, and going from there to write something more to my liking – and yours, I hope. Personally, I thought everything after Episode 34 more or less sucked, except for the Destiny Gundam. I start with the battle in the Indian Ocean, because I thought Heine deserved a much better death than what he got. After that I pick up immediately after the Battle of Berlin.

MAJOR DIFFERENCES:

-Kira will be bed-ridden for a long while after Angel Down. In my opinion, his injury(or near-total lack thereof) as portrayed in animation was complete BS, considering what happened to him. This version will reflect that, and of course there will be some significant plot changes as a result.
-Battles are going to be changed somewhat, especially those towards the end of the series, such as Orb and the battles in space. There will also be some changes to the Destiny Gundam, but nothing major, as well as some changes in characters that die/survive.

DISCLAIMER

I own SEED Destiny...

Yeah, right. I wish. I don't own this, it's just a fanfic...I don't know who owns this. Whoever does, this is how certain events in SEED Destiny would have turned out if I did own it. But I really don't own this.


Phase 01: Shadows of War (Phase 23)

"The LHM-BB01 Minerva...it is certainly a very impressive ship, very different from the Nazca-class." Heine Westenfluss, of the Supreme Council's Fast-Acting Integrated Tactical Headquarters, said as he looked around him. He was being given a tour by three of his new subordinates, Lunamaria Hawke, Shinn Asuka, and Athrun Zala, while maintenance personnel loaded his ZGMF-X2000 GOUF Ignited into the hangar. A prototype for the next-generation mass-produced mobile suit, it was fast and agile, and fairly well-armed.

-"Did you serve aboard a Nazca-class, Commander?" Lunamaria asked.

-"I was attached to the Hawkins Team during the last War. We were assigned to ZAFT military HQ until the first battle in this war, where I launched from the Waldegg." After a brief pause, he added, "I would appreciate it, Lunamaria, if you, and all the other pilots, dropped the formalities and called me Heine. It is my name, after all, and aren't we all soldiers? What, Athrun, is it you who has them all refer to me as 'Commander'? Whether you're in FAITH or not, whether your uniform is red or green, we're all pilots of ZAFT, and we should work together, as friends. Is that not so?" Athrun found himself wishing he were more like the Commander, and said so.

-"Excuse me? It's Heine. You aren't joking with me here, are you?" Heine asked, "Trying to give the new guy a hard time?" Athrun

-"I'm sorry, Com...Uhm, Heine"

-"See? Isn't that better?" The statement wasn't a question. They moved on, and as Athrun gave Heine the tour of the ship, the older Commander fell back and turned to Shinn. "Shinn Asuka. I've been meaning to congratulate you on your performance during the Battle in the Gulnahan Ravine."

-"You were there, sir? Heine?" Heine briefly smiled.

-"Don't call me 'sir', it makes me feel old. Yes, I was there. Commander Hawkins ordered us all to hold on, until you could reach the Lohengrin. It was my last battle in my ZAKU Phantom, and also with the Hawkins Team. So again, congratulations on a job well done."

-"Thank you, Heine!" Shinn answered, and the group moved on.

Meanwhile, a massive Orb fleet, led by the enormous flagship Takemikazuchi, was making its way around the Cape of Good Hope. In the command post of the Takemikazuchi, Colonel James Todaka(AN: It was bothering me that he didn't have a first name, so I picked one – I liked James, for him) was discussing his next move with Lieutenant Colonel Ichiro Amagi(AN: ditto for him. I picked his at random, though)

-"So, Colonel. Our orders are to link up with the Atlantic Federation fleet and get in touch with the John Paul Jones?

-"That's right, Amagi.

-"This is...Doesn't this deployment, so far from home, run counter to the ideals of Orb?"

-"I know. But I'm counting on Lady Cagalli and the Archangel to protect the ideals of our nation. I only hope they aren't too late."

Meanwhile, not far from the Black Sea, onboard the John Paul Jones, Colonel Neo Roanoke opened his new orders.
-"Use the Orb fleet, huh? Well, that sounds like a plan - we'll send them ahead of us in the Dardanelles"

In a dimly-lit back-room, three glass-canopied, circular beds stood surrounded by machinery. Two of these alone were open and empty. The third opened, and a slender blonde, wearing a short, white dress and clutching a pale-blue handkerchief tightly in her hand, stirred, and sat up.
She looked at the handkerchief, puzzled.

-"What's this?" For a second, she wasn't sure. She decided it was nothing, and set the handkerchief down on the bed as she stood and left.

"So then, we will go through the Channel, and attack from there." Talia Gladys finished her briefing on the attack, by all available ZAFT forces, on the Alliance facilities in the area around the Black Sea.

-"I'll go begin our launch preparations, then."

-"Yes, Arthur. Athrun?"

-"Yes, Captain?" the pilot addressed his commanding officer.

-"The reinforcement fleet the Alliance is expecting will soon arrive, which means we will almost certainly have to engage them as well. And these reinforcements are from Orb. Does that pose a problem for you?"

Athrun hesitated briefly. Behind him, Heine looked slightly concerned. That concern did not fade, even as Athrun answered.
-"No, it's...it's okay."

-"Very well. We leave for the channel tomorrow morning."

The next morning, as it headed up the channel, the Minerva found that the Orb fleet was waiting for them, and the Impulse and the Saviour launched.
Shinn, even as he finished docking his machine's four Flyers, forming the X56S Force Impulse, raised his rifle and blasted away two Astrays. One of Orb's new models fired at him. Blocking the shot, he moved the Impulse and shot that mobile suit down as well.

Athrun, meanwhile, took out another two of the new transforming models – MVF-M11C Murasames - in his faster, more powerful Saviour. The flagship, an enormous naval carrier, launched more mobile suits - every machine it held in its hangars, a mixture of the new Murasames and M1 Astrays fitted with bulky flight packs.
The Minerva, having verified that both its machines were out of danger, had turned to face the Orb fleet and begun charging its Tannhaüser positron cannon, when suddenly a rifle shot pierced the energy-charged barrel. Nine people were killed in the ensuing explosion, and the Minerva itself was severely damaged, though still capable of fighting. But the ship was forced to land on the water.

As Shinn and Athrun searched the skies, a black-and-white machine, which both pilots immediately recognized, flew down from the northwest.

-"The Freedom." Shinn's lip curled, and his eyes narrowed. Athrun, meanwhile, was shocked to see this machine, which, the last time he saw it, two years prior, had been a smoking, radioactive wreck.

-"Kira? Cagalli?" He cried as he recognized, in between the Freedom and the Archangel, a red-and-pink mobile suit, otherwise identical to the old Aile Strike.
Cagalli broadcast to everyone in range, asking that Orb stop the battle. Instead, the Orb fleet fired a volley of missiles at the mobile suit, and another at the Archangel, while the John Paul Jones launched its mobile suits.

In his cockpit, Shinn sneered at Cagalli Yula Athha's naive attempts to stop the battle. Then, he noticed incoming Earth Forces machines headed towards the Minerva. Even as Heine's GOUF launched, and Rey and Luna's ZAKUs took up defensive positions atop the catapults, behind the Tristan cannons, Shinn intercepted the enemy machines, hacking the first in half with his beam saber, then shooting down two more with the beam rifle he still held in his other hand.

Athrun, meanwhile, had his hands full in a heated duel with the Chaos. The two mobile suits traded blows from their beam sabers, and when Chaos launched its weapons pods, Athrun moved out of its line of fire, and fired his own Beam Cannons. One shot missed, but another would've blasted the Chaos apart, had he not blocked.
Redocking his pods, the Chaos's pilot began the duel at close-range again.

While all this was happening, Heine was dispatching enemy mobile suits with relative ease, his GOUF being faster and more agile than them. Suddenly, his threat receiver warned him that the Gaia was incoming.
He turned around to see it charging, its beam saber held high for a vicious attack - which never came, as he launched his Slayer Whip, the weapon curling around its forearm.
-"Heh...what did you think? This Mobile Suit's no ZAKU, pal! IT'S NO ZAKU!!" At Heine's command, a powerful electrical surge coursed through the whip, the current overloading the circuitry in the Gaia's forearm and causing it to explode, taking with it the Gundam's beam saber.

The Strike Rouge was still floating there, not doing anything, as Cagalli reminisced at length about her father's ideals, leaving the Freedom and a golden-yellow Murasame, piloted by Andy Waltfeld, to take out those enemy Mobile Suits, mainly Earth Forces models, which came too close. The Freedom's pilot aimed for their heads or arms, though several times, those machines he disabled, their pilot having lost control, subsequently slammed into the ocean.

Shinn, as the Freedom closes in to attack, fires the Impulse's beam rifle. The shot grazes its upper shoulder, but the Freedom flies right by, hacking off the Impulse's right forearm as it passes it.
-"BASTARD!" Shinn yells

Behind Shinn was Heine, who in turn fires his Draupnir forearm-mounted four-barrel beam machinegun at the Freedom, with greater success, as shots pepper the front of the Mobile Suit. However, he loses his right forearm as well.
-"Attacking everyone indiscriminately like that, who the hell d'you think you are, you cocky bastard!"
The GOUF still had its Tempest beam sword in its left hand, plus a second Slayer Whip and Draupnir.

The Battle continues. The Freedom, engaged by the enemy's Abyss, briefly tangles with it, before severely damaging it with its beam sabers, and continues engaging Earth Forces Machines, as Athrun once more engages the Chaos at close-range. Heine, meanwhile, uses his remaining Slayer Whip and Draupnir machinegun to continue to destroy attacking Earth Forces mobile suits.
Suddenly, he sees the Gaia raise its beam rifle, aiming at Shinn from behind. Swooping down in between them, he blocks the shot, but his shield is shot off. He retaliates with the machinegun on his left forearm, and closes in. His sword crosses the enemy's saber, and a duel begins. The GOUF manages to kick away the Gaia long enough for Heine to fire the Slayer Whip, obliterating the Gaia's remaining forearm. It switches to its Mobile Armor mode and ignites its wing beam blades, charging him down and firing its cannons. He dodges, passing to its left and peppering its flank with machinegun fire.

Together with Shinn, in spite of the younger pilot having lost his forearm, Athrun was continuing to take out Earth Forces mobile Suits.
However, Athrun was still preoccupied with the Archangel's appearance, and Cagalli's unheeded pleas for the battle to stop. In an instant of inattention, he failed to notice the Gaia come up behind him and fire - until Shinn kicked him aside, blocking the shot, and closing in on the Gaia to engage it at close-range.
-"Watch your back, will you?"

A voice suddenly cried out . A Windam had slipped past the Archangel's defense line, and the Strike Rouge, with Cagalli onboard, was going down, severely damaged. The yellow transforming model swooped down, dispatching the attacker with a rifle shot that penetrated from behind, just below its flight pack, piercing the cockpit.
Switching to Mobile Suit mode, it grabs the severely damaged torso of the MS and pulled it up. The hatch opens as the Gundam's red-and-pink colors fade to grey, and out comes the pilot, who stumbles into the other MS's open hand.
Then, dropping the grey carcass, the MS steadily made its way back to the Archangel.

Shinn slashed at the Gaia's right wing, but it used its boosters to pass right by, losing some altitude. Shinn was then engaged by another Alliance mobile suit. In the second it took to dispatch it, the Gaia came up behind him, and fired.
Shinn noticed too late - One shot missed, but the other slammed straight into the GOUF Ignited's cockpit, as the orange machine once again placed itself between its black enemy and its intended target.

-"NO!" Shinn screamed. Alerted by the cry and the flash of the explosion, Athrun looked up, briefly scanning the skies. He could not see Heine's GOUF anywhere, and the realization that it was the GOUF that had exploded hit him like a hammer-blow.
-"HEEINEE!"

In a daze, still gazing at the falling debris of his Commander's, no, his friend's Mobile Suit, Athrun hears the order to retreat - The Alliance Fleets had pulled back. He returns to the ship, followed by Shinn, and the Minerva continues up the channel, towards Tarcuius.