This is an alt-u version of the Gundam SEED Destiny anime. The theme diverges from true canon at the Battle of Berlin.
The Second Bloody Valentine War. It began with the Break the World incident; the remains of Junius Seven falling onto the world and devastating it. Although humanity survives, millions die as the massive chunks of debris smash into the ground at incredible speeds.
ZAFT and the Earth Alliance are once again at war. The Earth Alliance is led by the leaders of the Logos organization, their objective to wipe out all Coordinators while receiving great profit for themselves. ZAFT is led by Chairman Durandal, who appears to have sincere intentions.
In the beginning, ZAFT manage to achieve several victories against the Earth Forces, despite having three of their prototype Gundams stolen. However, with the development of the Destroy Gundam, and Phantom Pain's acquirement of the Destiny and Legend, ZAFT begin to suffer loss after loss.
The deployment of the Requiem weapon destroys several of the PLANTs, but ZAFT fight back and capture the weapon, using it to destroy Arzachel base. Durandal then attempts to use it to enforce his 'Destiny Plan'. This plan is met with resistance in the form of Orb and the two veteran ships, the Archangel and the Eternal. Durandal is killed when the Messiah is destroyed by Kira Yamato, pilot of the Strike Freedom.
However, while ZAFT was distracted fighting Orb, the Earth Forces gathered what remained of their space fleets. Led by Phantom Pain, they launched an attack on the PLANTs at the same time as the battle over the Requiem. Despite being outnumbered, the Earth Forces rallied behind the Destiny and Legend, defeating ZAFT's defenders and destroying the PLANTs in nuclear fire.
The war is over, the world now dominated by the Earth Alliance. Logos survives, slipping back into the shadows to control their Alliance puppet. However, the Alliance finds itself plagued by resistance factions, led by the remnants of ZAFT and Orb.
And how they differ from the canon.
Battle of Berlin - Destroy Debut
Shinn quickly learns the identity of the Destroy's pilot, his loyalties become divided. He decides to take out his confusion on the Freedom, distracting it for the rest of the battle. This allows the Destroy to seriously damage the Archangel and the Minerva, forcing them to retreat.
Durandal reveals his true plans, footage of the Berlin battle transmitted to the world. He claims it is Logos' fault that the war goes on. He states that ZAFT will fight to destroy Logos, so peace may return.
Operation Angel Down
The damaged Archangel is detected by ZAFT forces and chased, ZAFT intending to destroy the ship. All that there is to defend it is Kira and the Freedom. The Archangel suffers further damage during the chase and is almost destroyed before it can reach the ocean. But Kira sacrifices himself and the Freedom to protect the Archangel long enough for it to escape. The Freedom is destroyed, but Kira survives and is rescued from the water by the Archangel.
Civilians and militia rise up to find and destroy the leaders of Logos, while they are successful at taking out a number of the smaller leaders, the major minds behind Logos manage to escape and find protection inside their Earth Alliance puppet. Now that they are out in the light, they no longer have to secretly guide the Alliance.
To Catch a Thief - Gibraltar Base
The Earth Alliance learns about ZAFT's two newest Gundams and sends Phantom Pain to do something about them. Phantom Pain's extended are inserted with a commando team, using the arriving Earth Forces as a cover. They make it to the hangar storing the Legend and Destiny. They manage to board the two machines and break out, returning them to the Earth Alliance.
During the commotion, Athrun learns that Durandal plans to have him arrested for treason, claiming he provided the information to the Earth Alliance that allowed them to steal the new Gundams. With Meyrin's help, he avoids capture and steals a Gouf. Having scrambled in the Impulse to deal with the stolen suits, Shinn is retasked to shoot Athrun down.
The attack against the Earth Alliance's Supreme Command Center, Heaven's Base. Ultimately, while outnumbering the Earth Forces, ZAFT suffer badly at the hands of the Destiny, Legend, Destroys and anti-air Nibelung. While Heaven's Base and the Earth Forces take considerable damage, in the end they are able to force ZAFT to retreat.
Second Battle for Orb
Despite failing to destroy Heaven's Base and capture the Logos leaders there, Durandal believes he has damaged the Earth Forces enough to continue with his plans. He sends ZAFT to Orb, claiming they are harbouring Logos leaders. Little does he know he is indeed correct. Djibril has traveled to Orb in hopes of secretly reaching space, to continue his own plans.
Despite starting out with the advantage, ZAFT's attack turns for the worse when the Archangel and its forces show up to assist Orb. Even with the Minerva arriving to assist them, ZAFT could not defeat the combined forces including the Freedom and Justice. As a result, ZAFT are forced to retreat. Both sides come out of the battle in a weakened state and Orb is once again forced to rebuild.
To Play a Requiem
Djibril escapes to the Requiem weapon on the moon's surface. There he fires the weapon, destroying a number of PLANTs and killing hundreds of thousands of Coordinators in the process. The only reason the capital of PLANT was not destroyed is ZAFT's space forces, which have remained relatively untouched through the war up until this point.
ZAFT make a desperate attempt to prevent further destruction to the PLANTs. While their main lunar fleet engages the last of the Requiem's relay stations, the Minerva makes a hurried attempt on the Daedalus base, home of the Requiem weapon. While the lunar fleet is successful, preventing another strike on the PLANTs, the Minerva is too under equipped to deal with the Destroys at the Daedalus base, allowing the weapon to fire. A small part of what remained of the ZAFT lunar fleet is destroyed as the beam reaches the last relay.
With the assistance of the weakened lunar fleet the Minerva and its pilots are able to bring overwhelming force down on the Destroys, and finally capture the Requiem before it can fire another shot. Unfortunately, Djibril is able to escape to Arzachel.
With Djibril at Arzachel, Durandal orders the use of the Requiem weapon. As what remains of the ZAFT lunar fleet gathers nearby, the Requiem is fired. Most of the base is destroyed in the resulting explosion, along with a good percentage of the forces stationed there.
With the destruction of Arzachel and the death of Djibril, Durandal believes Logos and the Earth Alliance to no longer be a threat, despite their holdings on Earth.
In the Face of Destiny
Durandal introduces the Destiny Plan to the world, all the while preparing the Requiem and ZAFT's forces to quell any opposition to the plan.
For the Future
Urged on by the likely coming destruction of Orb, a combined fleet consisting of the Archangel, Eternal, Kusanagi, Orb forces, ZAFT forces, and Earth Alliance forces, launch an assault against the Requiem and its relay stations.
Weakened by its previous battles, ZAFT under the command of Dullindal still manage to field a large number of vessels and mobile suits, drawing some away from the PLANT's defenses. The battle quickly begins, with the Freedom and Justice pushing towards one of the relay stations with their METEORs. The Archangel then finds itself facing the Minerva yet again. The first of the relay stations is destroyed, but the battle still continues.
The Messiah effectively uses its 'Neo Genesis' weapon to deal a blow to the combined fleet, but the battle still continues.
Lacking the Destiny and Legend, the Minerva's aces are not able to withstand the combined might of the Freedom, Justice and Akatsuki. Although they put up a valiant fight, the three ZAFT aces are ultimately defeated. This leaves the three Orb aces to freely destroy the Requiem, Messiah and disable the Minerva.
The Destiny Plan dies with the death of PLANT Chairman Gilbert Durandal.
The Fall of the Hourglass
Unfortunately, both ZAFT and Orb had been focusing far too much of their attention on the happenings around the moon. Both the Requiem and the Messiah had proven to be a most effective distraction. Both sides had failed to accurately estimate the threat still posed by Logos and the Earth Alliance.
Half way through the battle over the Requiem, what remained of the Earth Forces Fleet were entering detection range of the PLANTs. At the head of the fleet was Phantom Pain, guided by the orders of a newly chosen Logos leader.
With the PLANT's defenses weakened by the transfer of ships for the fight over the Requiem, the following battle at the PLANTs proved to be a close one. But in the end, ZAFT failed.
Having previous knowledge of ZAFT's 'Neutron Stampeder', the Earth Forces fleet focused on a more conventional battle. ZAFT forces outnumbered the Earth Forces fleet, but all their aces were currently fighting the Orb threat. This left the regular forces to face the Destiny and Legend alone. Had Destroys been space capable, the battle would have been a slaughter. As it was, there was little which could threaten the two Gundams.
With communications to the Messiah cut, there would be no reinforcements. It was only a matter of time before the main defense lines fell and the Stampeders were destroyed. What followed was a terrible sight. Just thirty minutes after the destruction of the Requiem, the light of nuclear explosions lit the sky in the direction of the PLANTs.
The World as it is
With the destruction of most of the PLANTs, its leaders dead, its forces badly weakened, ZAFT falls into chaos. Most charge at Earth Alliance holdings, blinded by rage. They manage to inflict some damage before falling to the more organized defenses. Those few who are smart slip out of view of the public eye, to plan the destruction of the Alliance in secret.
Despite having suffered considerable losses, the Earth Forces are now the greatest power on and around the Earth. Those few countries not part of the Earth Alliance find themselves with no choice but to bow to them. Even Orb, in its weakened state, could not hope to stand against it.
Logos slips once again back into the shadows, content to let the general populace think they were destroyed. The Earth Alliance establishes itself as the planet's ruling power. With the Coordinator threat effectively neutralized, the Earth Alliance's leaders focus on rebuilding their reputation, claiming that those responsible for the actions of the Earth Forces during the war are no longer in positions of authority. Although there is initial disbelief, with no opposition to these words things soon calm down.