Plot
In May C.E.75, a one year after the end of the Second Alliance-PLANT War, remnants of the anti-Coordinator terrorist group, Blue Cosmos, continue to lead several attacks on Earth including PLANT-Aligned territories. A world peace monitoring organization, Compass under Orb Chief Representative Cagalli Yula Athha, former PLANT Supreme Council Chairwoman Lacus Clyne and President of the Atlantic Federation Foster, was formed to promote peace on Earth and PLANTs. The latter serves as its president. The organization's supreme commander, Kira Yamato, leads his team, consisting of Shinn Asuka, Lunamaria Hawke, and Agnes Giebenrath from the LHM-BB03S Millennium, to destroy the remnants on Afrika. At a meeting in the PLANTs, Lacus openly admits her hope to end the conflict swiftly and wishes to free Kira from it. On Earth, the government of the breakaway Kingdom of Foundation in Eurasia proposes a joint operation with Compass against Blue Cosmos. Lacus confides in Kira, and both agree to meet with the government to accept the operation.
The Millennium descends to Earth, accompanied by the battleship, LCAM-01XA Archangel, commanded by Murrue Ramius, and arrives in the kingdom. The government's Prime Minister, Orphee Lam Tao, and Queen Aura Maha Khyber, the leader of Foundation, meet the group. The members of Compass also meet the Black Knights, Foundation's mobile suit squad, but the team rebuffs them, showing off its superiority complex, earning disgusted looks from the group. On the Millennium, Agnes openly flirts with Kira, which Lacus overhears and runs away. Kira attempts to find her but is confronted by Orphee, who affirms that he is a more suitable partner to Lacus than Kira himself.
During the operation, Foundation turns on Compass and the Earth Alliance, with Orphee getting the Black Knights to draw Kira away. Kira's mind is telepathically overtaken by the Black Knights, who lead him to locate and pursue the Blue Cosmos leader, Michael. He crosses the demarcation line into Eurasia's territory unknowingly and, since Compass could only operate in the Eldore region, is attacked in retaliation. Branded as a traitor, Kira is overwhelmed by the Knights. Agnes betrays Compass and assists the Knights in defeating Kira. The Knights launch nuclear missiles from a hijacked Eurasia military outpost to destroy the kingdom and the government headquarters to frame Eurasia. The Archangel is ambushed and destroyed by the Knights, with Shinn also being defeated, but is rescued by Hilda. Thanks to the help of Athrun Zala, Meyrin Hawke, and Mu La Flaga, several crewmembers of the Archangel manage to survive the battle; however, Eldore and Foundation's capital, Ishtaria, are destroyed by the nukes, and Foundation leaders take Lacus to their base in space.
In the aftermath, Cagalli attempts to mediate between the PLANTs and the Earth Alliance but fails; both sides cut ties with Compass, and its activities are suspended. Athrun holds a meeting to reveal Foundation's true objective: to use Lacus and implement a variation of Gilbert Durandal's Destiny Plan, along with revealing the origins of Aura, Orphee, and Lacus, who are part of a new race of enhanced coordinators called the Accords, with Orphee and Lacus genetically designed to be their leaders and rule mankind together. Foundation reveals the repaired Requiem, destroys Eurasia's capital, Moscow, in revenge for the nuclear attack, and gives an ultimatum to the entire world and PLANTs: accept the Destiny Plan and their leadership within five days, or be destroyed. Kira breaks down, but Athrun convinces him to rejoin the fight, which he accepts. Compass then receives from Orb new versions of Destiny, Strike Freedom, and Impulse, and heads into space with the Millennium.
Meanwhile, Orphee attempts to seduce Lacus, but she rejects his advances and repeatedly tells him that he is not the person she chooses to love. Knowing that she is referring to Kira, Orphee becomes furious and continues to hold her hostage. A coup d'état occurs within ZAFT in support of Foundation, and a fleet is sent to protect Requiem. ZAFT members Yzak Joule and Dearka Elsman escape the coup and join the FFMH-Y101 Eternal to stop the rogue faction after evacuating the leader of the PLANT supreme council. An assault team led by Kira infiltrates Foundation's base on the Artemis asteroid and rescues Lacus, as Mu damages and disables the Requiem by reflecting its blast. From the Millennium's bridge, Lacus broadcasts a message, revealing the Foundation's true motives and condemning their actions.
Orb dispatches the Kusanagi to join forces with Millennium and Eternal, and heads into battle against Foundation. Orphee sorties with Ingrid in his mobile suit, overwhelming Kira along with Shura, but Athrun saves him and engages the latter with the new version of his Infinite Justice. Yzak, Dearka, the Eternal, and the Kusanagi suppress the rogue ZAFT fleet as Murrue leads the Millennium in destroying Aura's flagship. Lacus arrives and assists Kira in destroying all of the Foundation's mobile suits and ships in the newly-formed ZGMF/A-262PD-P Mighty Strike Freedom Gundam, piloted by both Kira and Lacus. Shinn and Hilda defeat the Black Knights, and Lunamaria disables Agnes. Athrun defeats Shura with Cagalli's help, and Shinn destroys the repaired Requiem, with support from Lunamaria and Athrun, moments before it could fire at Orb. Convinced by Lacus and Kira's beliefs about world peace and true love, Orphee and Ingrid accept their defeat, and the war ends. Lacus and Kira descend to Earth on a beach, where they share a kiss.
