地球聯合軍和札夫特軍在雙方均傷亡慘重的二次雅金・杜維攻防戰一役後，於尤尼烏斯七號的遺跡締結了停戰條約，然而此舉仍無從撲滅自然人和調整者之間的爭鬥火種。 C.E.73年10月。在化名為亞歷士．迪諾的阿斯蘭・薩拉陪同下，卡佳里・由拉・阿斯哈以歐普代表首長身分造訪了在L4新設置的札夫特PLANT「軍械庫一號」。有鑑於雙方陣營再次出現不穩定的情勢，因此她們前往該處與最高評議會的會長吉伯特・杜蘭朵進行極機密會談。 此時突然警報大作！ 一個神秘組織鎖定了新造船艦「智慧女神號」的下水典禮展開破壞活動，更趁亂搶奪了即將出廠的新型MS「鋼彈」。 面對再次燃起的戰火，卡佳里感到混亂不已。在一片爆炸煙霧中，阿斯蘭為了保護她而搭乘了MS「薩克戰士」，力抗被敵方奪走的混沌鋼彈、蓋亞鋼彈，以及深淵鋼彈。可是由於寡不敵眾，加上敵方機體的性能遠勝於己，二人因此陷入了絕境！ 在千鈞一髮之際，一架新型MS介入其中。 那架機體正是由真・飛鳥駕駛的脈衝鋼彈。

神秘組織突然在PLANT「軍械庫一號」搶奪了「鋼彈」。為了和札夫特新議長吉伯特．杜蘭朵會談而來到這裡的歐普代表首長卡佳里・由拉・阿斯哈，以及陪伴她前來的阿斯蘭・薩拉均被捲入這場危機中。 為了保護卡佳里，阿斯蘭緊急駕駛了一架薩克戰士力抗三架被奪走的鋼彈，惟因不敵而陷入困境。就在千鈞一髮之際，真・飛鳥駕駛著脈衝鋼彈介入戰局。 脈衝鋼彈與混沌鋼彈、蓋亞鋼彈、深淵鋼彈展開了激烈交鋒！ 與此同時，在指揮官尼歐・羅安那克的指揮下，從軍械庫一號外圍派遣人員潛入內部搶奪鋼彈的特殊部隊母艦「葛蒂．露號」也展開了行動。該船艦發動閃擊戰將札夫特的護衛艦給擊沉，更破壞了港口部位。 有如呼應該船艦的行動般，搶奪部隊的成員史汀格・歐格雷、奧爾・尼達和史黛菈・路歇開始撤退。三架鋼彈打破了PLANT的外壁試圖逃脫，雖然脈衝鋼彈和雷・札・巴雷爾駕駛的薩克幽靈展開追擊，不過尼歐所駕駛的MA「艾格薩斯」早已在太空中等著他們。 面對此等突發事態，札夫特新型船艦「智慧女神號」的艦長妲莉雅・古拉迪斯決定啟航出擊

After the Minerva launches from Armory-1, the battle against the Girty Lue ends, for the time being. However, Girty Lue launches another attack preventing the crew from having much time to regroup.

During the battle with the Girty Lue, Athrun helps the Minerva out of a bind with his strategizing.

As Junius-7 plummets towards the Earth, the Minerva team-up with the Joule team to try and destroy it.

The battle on Junius-7 instifies, as the Gaia, Chaos & Abyss make the Joule team's attempt at the destroying the falling colony much more difficult.

As a last ditch effort, the Mireva uses is Tanhäuser to break up the remaining chunk of Junius-7. Unfortunatey, several of the pieces fall to Earth destroying several of Earth's cities. The battle-damaged Minerva makes its way to Orb to re-supply and to drop Cagalli off.

The Minerva arrives at Orb. While the crew enjoys some downtime. Cagalli learns some unsettling information about the future of Orb. While Athrun decides to return to PLANT once more and meet with Dullindal.

Eager for retaliation, the Atlantic Federation declares war on ZAFT (who they blame for the Junius-7 drop). In defense of the oncoming nuclear onslaught, ZAFT unleashes its newest weapon, the Neutron Stampeder, against the Atlantic Federation forces.

As Athrun meets with Dullindal, the Dullindal-endorsed psedo-Lacus, Meer Campbell, rallies the citizens of the PLANT's look away from war and look towards peace. Later, Dullindal offers Athrun a chance to pilot one of ZAFT's newest mobile suits, the ZGMF-X23S Saviour.

Orb decides to ally itself with the Atlantic Federation, much to Cagalli's dismay. While about the PLANT's, Athrun recieves some help making his decision from some old comrades.

After departing Orb, the Minerva is thrown into battle against an Atlantic Federation fleet. Due to their new alliance with the Federation, Orb quickly sets up a baracade of ships preventing the Minerva from retreat back to the safety of Orb territory.

As the Minerva's crew congratulates Shinn on his job well done, Kira is forced to take the Freedom out into battle once again to take out the assassins that are after Lacus.

Kira, Lacus, and the remaining Archangel crew embark on their old vessel and depart, but not before Kira rescues Cagalli from her wedding to Yuna.

Athrun, now a member of the super elite ZAFT task force FAITH, returns to the Minerva. Once aboard, he delivers the Minerva's new mission to Talia.

The Minerva engages Neo and the 3 stolen Mobile Suits in a battle over the Indian Ocean.

The Minerva lands at ZAFT's Muhamal base and gets details on their next assignment. Later, Athrun has a "heart-to-heart" conversation with Shinn.

The Minerva must destroy a fixed positron cannon emplacement to break through to Gibraltar. Though hesitant at first after meeting Shinn, they are helped by a young resistance fighter named Coniel, who provides data of a secret tunnel that will lead near the positron cannon. The Minerva and the other ZAFT forces draw out the Earth Alliance mobile suits and mobile armor while Shinn heads through the tunnel and destroys the cannon.

Shinn narrates flashbacks covering the events that have transpired in Gundam SEED and SEED Destiny. He also sheds some light on how he got to the PLANT's after his tragic loss in Orb.

After a misunderstanding between Athrun, Lunamaria and Meer, Shinn takes advantage of his shore leave by exploring the countryside. On his travels he stumbles across Stellar dancing on a cliff, she then accidentally falls into the sea. Shinn dives in after her. While waiting to be rescued, Shinn and Stellar share some bonding time.

An EA fleet led by Orb forces heads towards to Black Sea to deal a critical blow to ZAFT. However, a third party is waiting in the wings to stop the battle.

Cagalli's attempts to stop the Orb fleet fails and a battle between the Minerva, Orb/EA fleet and the Archangel breaks out.

With Milliaria's help, Athrun is able to meet up with Kira and Cagalli to discuss recent events.

With Milliaria's help, Athrun is able to meet up with Kira and Cagalli to discuss recent events.

Shinn rushes an injured Stella aboard the Minerva. Once aboard, he learns startling information about Stella. Elsewhere, Lacus decides to go to PLANT and scope the situation out.

In Space, Lacus & Andy reunite with the Eternal and its crew. Lunamaria reports her findings from Athrun's rende-vous with Kira to Talia as Stella's condition worsens. Elsewhere, Miriallia rejoins the Archangel and decodes a message that informs the group of an upcoming battle between Minerva and Orb/Phantom Pain.

All hell breaks loose in a three-way battle between the Minerva, Orb/Earth fleets and the Archangel.

As Dullindal plays a lonely game of chess, he reflects upon the past and the philosophy of his dear friend, Rau Le Crueset.

In order to save Stella's life, Shinn brings her back to Neo.

Shinn and Rey both receive pardons for freeing Stella, a Prisoner of War, much to Talia and Athrun's surprise. Meanwhile, a revitalized Stella pilots the EA's new heavy assault MS, the GFAS-X1 Destroy, and wipes out several villages on the Russian front.

The Minerva and Archangel work to stop the Destroy and its destructive rampage through Europe. Shinn is shocked to learn that Stella is the unit's pilot.

Shinn, swearing vengeance on the Freedom, studies up on it with hopes of defeating the MS that killed Stella. Meanwhile, the Earth Sphere is thrown into chaos as Durandal announces to the world that Logos is behind the war and this never-ending hatred.

As the Archangel makes its way towards Orb, it is attacked by the Minerva. Having studied up on the Freedom, Shinn prepares to destroy it.

As the Archangel crew scrambles to stabilize their ship, Cagalli rescues an incapacitated Kira. Aboard the Minerva, Shinn gloats to Athrun about his victory. Dullindal decides to make his way toward Earth to present two new mobile suits to Athrun and Shinn...

After his less-than-warm reception to Dullindal, the Destiny and the Legend, Dullindal decides that Athrun will only hinder his goals. With Special Ops soldiers after his life, Athrun decides to, once again, leave ZAFT.

Shinn is reluctant to shoot down Athrun's Gouf. However, Rey manages to relieve him of his doubts and convinces him to shoot down Athrun and Meyrin!

ZAFT leads an offensive on the EAF's Heaven's Base in hopes of defeating Logos.

After a trip to the Mendel Colony, Lacus and the Eternal's location is discovered by ZAFT. Just when it looks bleak for the Eternal, Kira comes to the rescue...

After Zaft's ultimatum requesting Djibril, Yuuna gives the obvious lie of Djibril not being in Orb in a public announcement. Following the announcement, Zaft begins its invasion of Orb. Cagalli is given her father's will: the mobile suit Orb-01 Akatsuki, arrests Yuuna and reforms Orb's defense against Zaft. Later, the Minerva arrives and Destiny launches to confront the Akatsuki...

Athrun and Kira share their thoughts of what has happened during the war.

Athrun and Kira recall the past events from their perspective and explain why they follow the paths they have chosen.

As the attack on Orb continues, Cagalli faces off against Shinn. She is saved by the timely arrival of Kira who descended from space with Lacus. Shinn is forced to retreat to resupply. While Kira continues to destroy ZAFT forces, Lacus shows Athrun the ZGMF-X19A Infinite Justice and gives him the decision to choose whether he wishes to stay away from the battle or become a soldier again and fight for what he believes in.

Athrun intervenes in the battle between Kira, Shinn, and Rey, which shocks Shinn who believed that he had killed Athrun previously. Yuna is crushed by a GOUF Ignited when he tried to escape while Djibril successfully escapes to the Moon aboard an orbital shuttle. With the ZAFT flagship destroyed, Captain Gladys takes command and orders a temporary retreat. After the battle, Cagalli broadcasts a global announcement about the war with Logos but she is interrupted by Meer, who is in turn interrupted by the real Lacus.

The real Lacus on television states that there is someone who has the same face, voice and name as herself in the PLANTs. She also states that people should find out more about Chairman Durandal's actions before believing in his lies. Djibril arrives at the Daedalus Lunar Base, where he fires the Orbital All-Aspect Tactical Cannon, Requiem, at the PLANT capital, Aprilius. The attack on Aprilius fails, but Januarius One through Four is hit, and they collide into December Seven and Eight causing them to collapse also. The Minerva returns to space.

After the attack on the PLANTs by the Requiem, the Orb forces begin their preparations to leave Earth. ZAFT begins their assault on Requiem and the Minerva is sent to the front lines. Lunamaria is given the task of destroying Requiem's controls while the Destiny, the Legend, and Minerva divert the enemy's attention away from her. The Destiny and the Impulse destroy Requiem's controls. Djibril attempts an escape on the Girty Lue, but Rey discovers him and destroys the Girty Lue. Cagalli parts with the crew of the Archangel and watches the ship leave for the Moon.

While gathering intelligence under the guise of a shopping trip at Copernicus City, Lacus receives a message from Meer, who is afraid of being killed. Though Athrun and Meyrin insists it is a trap, Lacus decides to meet Meer anyway. The would-be assassins are killed, but Meer is mortally wounded.

A funeral is held for Meer on the Archangel. Athrun, Kira, Lacus, and Meyrin read Meer's diary and learn why she had aided Durandal.

Chairman Durandal calls for the implementation of the "Destiny Plan", which is supposed to decide the fate of each individual on a genetic level. Only the Orb Union, the Kingdom of Scandinavia, and the Atlantic Federation reject this plan. ZAFT repairs Requiem and fires it at the Earth Alliance lunar base of Arzachel, killing the President of the Atlantic Federation. Terminal forces head towards Relay Station 1 of Requiem.

Kira in the Strike Freedom is confronted by Rey in the Legend. Meanwhile, Athrun in the Infinite Justice battles Lunamaria in the Impulse and Shinn in the Destiny. Requiem is destroyed in a joint effort of the Infinite Justice and Mu in the Akatsuki. The combined efforts of the Archangel and the Infinite Justice, damage the Minerva, causing it to crash onto the Moon. Durandal and Kira confront each other in the collapsing Messiah. Durandal is shot by Rey, and Captain Gladys orders Kira to leave as she, Rey and Durandal are killed when the Messiah falls to the Moon surface. The Second Bloody Valentine War ends.