Two years after the conclusion of Mobile Suit Gundam Seed, a new chapter in the saga of the Cosmic Era begins. Gundam Seed Destiny introduces a new cast of heroes, in the form of Shinn Asuka and the crew of the ZAFT warship Minerva, as well as a number of returning characters from the previous series.

In Gundam Seed Destiny, we learn that the tensions between Earth and the PLANTs have continued even after the end of the previous war, and it seems almost inevitable that this brief interval of peace will soon give way to a new conflict. Is humanity doomed to endlessly repeat this cycle of war and hatred, or is there a way to break the chain and establish a lasting peace? And if so, will it be worth the cost?


In year 72 of the Cosmic Era, the Junius Treaty brought the hostilities between ZAFT and the Earth Alliance to a formal conclusion. The treaty banned all military use of nuclear weapons and nuclear power, and placed strict limits on the size of the ZAFT and Earth Alliance forces. However, there are still tensions between the genetically enhanced Coordinators and the unmodified Naturals, and the peace between them remains fragile.

In October of C.E. 73, Cagalli Yula Athha, chief representative of the neutral Orb Union, arrives at the ZAFT military station Armory One. She is accompanied by her bodyguard, the former ZAFT soldier Athrun Zala, who now goes by the alias Alex Dino. Cagalli meets with Chairman Gilbert Durandal of the PLANT Supreme Council to voice her concerns about ZAFT's recent arms buildup. Their conversation is interrupted as mysterious intruders attack Armory One and capture three of ZAFT's newest Gundam mobile suits.


With Armory One under attack, Athrun commandeers a ZAFT mobile suit to get Cagalli to safety. The three captured Gundams engage Athrun's ZAKU in combat, but he is rescued by the sudden appearance of the young ZAFT pilot Shinn Asuka and his Impulse Gundam.

Outside Armory One, the enemy mothership Girty Lue joins the battle and wipes out the ZAFT defense fleet. Shinn and his comrade Rey Za Burrel attempt to pursue the stolen Gundams as they escape from Armory One, only to find the enemy commander waiting for them in the darkness of space.


Shinn and Rey struggle against the enemy commander Neo Roanoke. In order to help her pilots, ZAFT Captain Talia Gladys orders the newly constructed warship Minerva to launch from Armory One and join the battle. The enemy forces withdraw, and the Minerva gives chase.

Although Cagalli and Athrun have ended up aboard the Minerva, the apologetic Chairman Durandal informs them that there is no time to send them home to Orb. Durandal gives Cagalli a tour of the ship, and she reacts with anger to the sight of ZAFT's new weaponry.


The Minerva follows the Girty Lue into the debris belt that surrounds Earth, and sends Shinn and his comrade Lunamaria Hawke in pursuit of the enemy mothership. However, Neo has tricked the ZAFT pilots into following a decoy. While the three stolen Gundams ambush Shinn and his comrades, the Girty Lue doubles back to attack the undefended Minerva.

Just as all seems hopeless, Athrun devises a plan to help the Minerva escape from the enemy trap. Neo recalls his forces, and the battered Minerva is forced to abandon its pursuit. It seems as if the fighting is finally over, but an even greater crisis is already developing.


Aboard the Minerva, Chairman Durandal receives shocking news. The ruins of Junius Seven, the PLANT that was destroyed in the infamous Bloody Valentine incident and where the armistice treaty was later signed, have left their stable orbit and begun falling towards Earth.

ZAFT swiftly dispatches a demolition crew commanded by Yzak Joule to break up the remnants of Junius Seven, but it becomes clear that this is no mere accident when the demolition crew is attacked by what appear to be ZAFT mobile suits. As the Minerva arrives at Junius Seven to provide support, Athrun volunteers to join the battle.


The Minerva launches its mobile suits to support Yzak and his demolition crew. Shinn, Rey, Lunamaria, and Athrun join the battle against the mysterious group who have sent Junius Seven falling towards Earth. The situation becomes even more chaotic as the Girty Lue arrives and the stolen Gundams enter the fray.

In the middle of all this fighting, the demolition crew complete their work and break up the ruins of Junius Seven. The Minerva follows the remaining fragments into the atmosphere in order to break them up even further, while Shinn and Athrun continue fighting the last of the mysterious mobile suits and confront the enemy leader.


Despite the heroic efforts of its crew, the Minerva has been unable to avert disaster, and the fragments of Junius Seven inflict terrible damage as they fall across Earth's surface. The Minerva retrieves Shinn and Athrun as they descend to Earth, then sets course for Orb in order to return Cagalli and repair the damage it has suffered in its space battles.

Meanwhile, the anti-Coordinator group Blue Cosmos is already moving to take advantage of this disaster. Lord Djibril, the new leader of Blue Cosmos, confers with the other members of the Logos secret society to plan their response.


Once the Minerva arrives in Orb, Cagalli resumes her duties as Chief Representative. Her prime minister, Unato Ema Seiran, tells her of the damage caused by the fall of Junius Seven and urges her to approve an alliance with the Atlantic Federation.

The engineers of Morgenroete begin repair work on the Minerva, supervised by the former Archangel captain Murrue Ramius. Athrun meets with his old friends Kira Yamato and Lacus Clyne, who have taken refuge in Orb after their island home was flooded by the fall of Junius Seven. At last Athrun decides to return to space to meet with Chairman Durandal, leaving Cagalli with an unexpected parting gift.


The Atlantic Federation and its allies declare war on the PLANTs in response to the fall of Junius Seven. Although Chairman Durandal still hopes for a diplomatic solution, the ZAFT forces are mobilized to defend the PLANTs. Yzak and his comrade Dearka Elsman join the battle only to discover that they are fighting decoys while the Earth Forces attack the PLANTs with nuclear weapons.

As the battle rages, Athrun waits on the sidelines for a chance to talk to Durandal. He is surprised to encounter a young woman who looks just like Lacus, and is even more stunned when the impostor greets him as if they were long-separated lovers.


Chairman Durandal tells the horrified Athrun the details of the Earth Forces' latest attack on the PLANTs. Giving up his Alex Dino alias, Athrun admits his true identity and begs Durandal not to let this conflict escalate into another war. As the citizens of the PLANTs call for revenge, the impostor Lacus Clyne appears on their screens to calm their anger.

Durandal admits that he has created a false Lacus to influence the PLANT citizens, and tells Athrun that he wishes to make use of his strengths as well. After offering Athrun the use of a powerful new Gundam, Durandal leaves him to consider his options. Meer Campbell, the Lacus impersonator, meets Athrun again and invites him to dinner.


The conflict continues to escalate as Earth Forces fleets encircle the ZAFT bases at Gibraltar and Carpentaria, and the PLANT Supreme Council decides to strike back in the name of self-defense. Despite her best intentions, Cagalli yields to her ministers' demands that Orb ally itself with the Atlantic Federation. The Minerva receives a warning message and prepares to leave Orb before it is too late.

In the PLANTs, Athrun visits the grave of his old comrade Nicol Amalfi. He is escorted by Yzak and Dearka, who urge him to return to the ZAFT forces. And back in Orb, Cagalli faces a fateful decision of her own.


The Minerva crew find an Earth Forces fleet waiting for them outside Orb's territorial waters, leaving them no choice but to somehow break through the enemy lines. While Rey and Lunamaria guard the ship, Shinn fights an aerial battle against the Earth Forces mobile suits, but the tide turns against them as the enemy deploys a huge mobile armor whose positron deflector shield can withstand even the Minerva's Tannhauser cannon.

Meanwhile, Athrun has finally decided to rejoin ZAFT. Chairman Durandal makes him a member of the elite special forces organization known as FAITH, and Athrun departs for Earth in the Saviour Gundam.


Thanks to Shinn's fighting prowess, the Minerva has overcome the Earth Forces fleet. As the ship continues on to Carpentaria, the Orb government concludes its alliance with the Atlantic Federation. Yuna Roma Seiran, the son of Orb's prime minister, pressures Cagalli to accept his marriage proposal in order to unite their nation.

Now that Orb has aligned itself with the Earth Forces, Kira and his friends are considering leaving for the PLANTs. But their plans are disrupted when their home is attacked by Coordinator special forces who have been sent to assassinate Lacus, and Kira is forced to enter the battlefield once again.


In the wake of the assassination attempt on Lacus, Kira and his friends realize that they have been targeted by the government of the PLANTs. Kira then receives a letter from his sister Cagalli, in which she tells him of her intention to marry Yuna and asks him to return Athrun's ring on her behalf. At last Kira decides on a course of action.

Though she is still haunted by thoughts of Athrun, Cagalli has resigned herself to a loveless marriage. But as the ceremony begins, Murrue and her comrades launch the rebuilt Archangel, and Kira takes flight in the Freedom to save Cagalli from this grim fate.