Shinn and his family were Coordinators living on the Republic of Orb until the Alliance invaded the nation where his family died in the crossfire during the Bloody Valentine War.
After the tragedy, Shinn was sent to the PLANTs by an Orb official and there he joined the ZAFT Academy to get the power he needed to protect everyone he cares.
Two years after the Bloody Valentine War ended, he graduated from the Academy with his friends and was going to be the test pilot of ZAFT's Impulse Gundam, however, he is forced to use the Gundam after Phantom Pain, a trio of pilots from the Earth Alliance, steals three of the four Gundams made by ZAFT by orders of Neo Raonoke, an mysterious masked man, Shinn in the Impulse Gundam manages to force Phantom Pain out of the colony as Neo ordered an retreat.
Eventually, Shinn and Rey are ordered to fall back to the Minerva. On board, Shinn is shocked to learn that Athrun had saved him from the Extendeds. He also is irritated to learn that Cagalli is on board as well, for he blames his family's deaths on her father, Uzumi Nara Athha, and he shows this readily in Cagalli's presence.
The Minerva is ordered to aid the Joule Team with the demolition of Junius Seven, which is on a collision course with Earth. This is caused by a rogue ZAFT force that supports the late Patrick Zala. The Minervapilots, the Joule team, and Athrun kill the terrorists and drive off the Extendeds, but only partly succeed in their demolition efforts. During re-entry, Shinn saves Athrun, whose heavily damaged mobile suit was in danger of being destroyed.
After returning Cagalli and Athrun to Orb, the Minerva is stationed at Orb for repairs during this time Shinn goes to visit the place where his family died at Orb's memorial he then meets Kira Yamato and Lacus Clyne without knowing who they are. During the confrontation Shinn and Kira talk only to have Shinn telling Kira that no matter what happiness there is, people will destroy it again.
The Minerva then leaves quickly because Orb is about to join the Earth Alliance Forces. Yuna Roma Seiranand his father plan to offer them to the Earth Alliance fleet waiting outside Orb territory, and Yuna deploys the Orb fleet to prevent the Minerva from reentering Orb. Because of an unexpected fight, Minerva is severely damaged and is also in a downside situation. With the Impulse, Shinn battles the massive mobile armor YMAF-X6BD Zamza-Zah created by the Earth Alliance Forces. However due to its new technology, the Impulse runs out of energy. With rage and anger, thinking that he has to still avenge his family, Shinn awakens Seed Mode for the first time. Using Seed Mode, Shinn saves the Minerva and also destroys nearly every Earth Alliance ship. Shinn starts to be recognized by enemies and starts to become a ZAFT ace.
While stationed in Diocuia, Shinn saves Stella from drowning after she falls from a cliff into the water. Stella becomes frantic when Shinn yells at her for being careless, asking her "Are you trying to die, you twit?!" Stella panicked when Shinn accidentally said her block word, "die", Shinn tries to assure Stella that no one was going to hurt her, she became more scared. Stella yelled out to Shinn that she was scared to die. He grabs her and gives her a hug, telling Stella that she won't die. He tells her that he will protect her. Stella, hearing the same thing that Neo had said, starts crying in Shinn's arms. To calm her, Shinn swears to protect her. They are stuck at the bottom of the cliff until a ZAFT boat arrives to rescue them. They become closer, but when Stella returns to Phantom Pain, her memories of Shinn are erased.
Following the addition of Heine Westenfluss and his ZGMF-X2000 GOUF Ignited, the Minerva is attacked by Phantom Pain and the Orb fleet commanded by Yuna Roma Seiran. The ZGMF-X10A Freedom, piloted by Kira Yamato, and the Archangel intervenes. Kira damages the, LHM-BB01 Minerva, Impulse, the GOUF, and other mobile suits. Heine and his crippled GOUF are sliced in half by the Gaia when he unknowingly moves between it and the Freedom. Since the Freedom intervened, Shinn has been wanting to defeat the Freedom as he was awed by its abilities. Heine's death angers both Athrun and Shinn.
The Minerva is sent to investigate the Extendeds facility in Lodonia, the place where the Extendeds are created and trained. Shinn becomes even more angry with the Earth Alliance's Blue Cosmos leaders, asking how can they say tampering with genes is wrong when they do things like this.
The Minerva heads for Gibraltar, but they are intercepted again by Phantom Pain and the Orb fleet commanded by Yuna Roma Seiran and Captain Todaka. The Archangel intervenes and Cagalli Yula Athha gives a speech, which angers Shinn, who fires at her. Kira destroys the missiles and attacks Shinn. Shinn goes into SEED mode and destroys the Abyss, killing its pilot, Auel, and decimates the Orb mobile suit force. Shinn then directly engages the Orb fleet, sinking several ships. Captain Todaka, is killed when Shinn attacks the Orb carrier Takemikazuchi.
Afterward, Shinn overhears his commander's discussion which concludes that the Extended prisoner Stella will die without the right medical treatment, and her body will be transported to a ZAFT science facility for dissection and testing to study the Extended program. Horrified, Shinn decides to return Stella to the Earth Alliance, and does so with Rey's help. Both are confined as punishment and could have been executed, but are released on Gilbert Durandal's orders.
Stella is designated as the pilot of the transformable mobile armor GFAS-X1 Destroy, and goes on a rampage leveling several cities in Western Eurasia territories that have sided with ZAFT - as an object lesson. She is intercepted by ZAFT over the city of Berlin, but Berlin is heavily damaged and ZAFT forces there are obliterated. Soon after, the Archangel and its mobile suits arrive and battle the Destroy, much to the surprise of the Minerva, which arrives shortly afterwards.
Kira in the Freedom engages the Destroy and is joined by Shinn in the Impulse. When Shinn cuts open the Destroy's cockpit, Neo tells Shinn that Stella is the pilot. Shinn's feelings stop him from finishing the Destroy, and Stella's feelings for Shinn cause her to stop fighting, too. But when the Freedom approaches, Stella panics and prepares to fire the Destroy's chest beam cannons. Kira stabs his beam saber through the Destroy's cannons, causing a chain reaction that destroys the giant mobile armor and mortally wounds Stella. Stella tells Shinn that she loves him and dies in his arms, and Shinn cries out in anguish.
During this period of time the Chairman Durandal presents a speech around the entire world about the organization Logos and claims that by destroying them the war will end, and Shinn easily agrees, later when the Minerva is ordered to subdue the Archangel in the mission code-named "Operation Angel Down", Shinn gets his opportunity for revenge. After receiving the message that Archangel won't surrender, Shinn sees the Freedom. Shinn takes off on the Impulse and starts to fight Kira. Using the analyzed information from Rey that Kira will not attacks people's cockpits, Shinn and Rey devised a plan that will shut down the Freedom's attacks. Kira however activates Seed Mode and cripples the Impulse. However, all backed up and ready, Shinn immediately uses the 2nd Force Silhoutte to repair back the damage. With time running out and Shinn becoming more and more harder to defeat, Kira decides to run. The Minerva then shoots the Tannhäuser Cannon at the Archangel causing an explosion which made Kira falter. Taking chances, Shinn who also called in the Sword Silhouette, charged in and aimed straight at the Freedom's cockpit, destroying the Freedom. Afterwards, Shinn is shown with tears, too happy that he defeated probably the No.1 Gundam and also avenging Stella's death. Unknown to Shinn, Kira survives the ordeal.
When Shinn returns to the Minerva after destroying the Freedom, his comrades cheer him. Shinn tells Athrun that he defeated Freedom and killed its pilot, avenging Stella’s death and Athrun’s defeat. Furious by Shinn's rejoicing at the apparent death of Kira, a distraught Athrun punches Shinn in the face. Athrun adds that Shinn killed Kira but Kira never wanted to kill him. Rey counters that destroying Freedom and theArchangel was a direct order from ZAFT's headquarters, that all of them, including Athrun, were obligated to obey.
Back on the PLANTs, Durandal sends Rey and Shinn to hunt down Athrun. Rey tells Shinn that Athrun is a defector working for Logos and that Meyrin is an accomplice, not a hostage. When Rey and Shinn catch up with Athrun, Rey starts to fight Athrun. Shinn initially tries to persuade Athrun to return to ZAFT. Athrun refuses and tries to persuade Shinn not to fight, or to at least let Meyrin go. Shinn accuses Athrun of betraying their trust and stabs Athrun's GOUF Ignited with his beam sword, causing it to crash into the ocean and explode.
Unknown to Shinn and Rey, Ledonir Kisaka rescues Athrun and Meyrin. Shinn is shown to be sad and conflicted, believing he killed Athrun and Meyrin. He apologizes to Lunamaria and cries with her, though he feels his action was necessary to achieve the Chairman's goal of peace.
After some comforting by Chairman Durandal, Shinn prepares for the assault against Logos' Heaven's Base Headquarters in Iceland. In the Minerva mobile suit hangar just prior to "Operation Ragnarok", he encourages Lunamaria about her first sortie with the Impulse, and they console each other about Athrun and Meyrin's deaths. Both blame Logos for the apparent betrayal by Athrun and Meyrin. Shinn kisses Lunamaria and promises to protect her.
Shinn enters the battle and goes into SEED mode. With the help from Rey in the Legend and Lunamaria in the Impulse, Logo's five Destroy units are destroyed. Heaven's Base surrenders and both Talia (Minerva's captain) and Arthur Trine (Minerva's executive officer) are impressed by Shinn's battle skills. Chairman Durandal is obviously pleased by Shinn's victory.
A few days later, Shinn has nightmares about Stella's suffering, his fights against the Freedom, the killing of Athrun and Meyrin, and the battles against Logos. Rey tells Shinn that he did the right thing because they were all ZAFT's enemies. PLANT Supreme Council awards a second Nebula Medal to Shinn for his performance in Operation Ragnarok and Supreme Council Chairman Durandal appoints both Shinn and Rey to FAITH. After confirmation that the Seirans (the rulers of Orb at the time) are providing sanctuary to Lord Djibril, ZAFT initiates "Operation Fury", a full-scale assault on Orb in order to capture Lord Djibril.
Using the privileges as a member of FAITH, Shinn launches alone from Minerva in his Destiny and faces Cagalli in the ORB-01 Akatsuki. Shinn attacks the Akatsuki, identifying it as the leader, knowing that destroying it will demoralize the Orb defense, but Kira arrives in the ZGMF-X20A Strike Freedom and protects Cagalli. Shocked and enraged that the Freedom has survived, Shinn attacks the Strike Freedom. The two engage in extended battle until Rey orders Shinn to return to the Minerva to resupply and recharge. After this, Shinn and Rey launch to face the Strike Freedom together.
Athrun arrives in the ZGMF-X19A Infinite Justice. Shinn is surprised that Athrun survived their last encounter. Athrun demands that Shinn stop attacking Orb and questions the motives of the war. Believing that Athrun is a traitor, Shinn goes into SEED mode and attacks. Shortly thereafter, Minerva Captain Gladys orders the retreat of all ZAFT forces, including Shinn and Rey.
Cagalli's broadcast from Orb is interrupted by Meer (speaking as Lacus Clyne). But then Meer is interrupted by the real Lacus, leaving the crew of the Minerva confused. Shinn asks Rey for his opinion. Rey replies the enemy is using another "Lacus Clyne" as a psychological weapon. Rey then discusses Athrun's survival with Shinn. Lunamaria wonders if her sister Meyrin survived as well and Rey states that she is likely on the Archangel. This conversation upsets Shinn.
Later Lord Djibril unleashes Requiem and destroyed some of the PLANTs, both Shinn and Rey blame Kira and Athrun for their interference, Rey in particular blames Lunamaria for her failure to shoot down Djibril however Shinn quickly defends her.
The Minerva is ordered to attack the Requiem and the Daedalus base. Shinn is concerned for Lunamaria's safety for she has been given the mission to destroy the Requiem's controls but she convinces him to believe in her. Shinn in the Destiny and Rey in the Legend act as decoys and cripple the defenses of the lunar stronghold. Lunamaria in the Impulse destroys the Requiem's firing controls and Rey kills Lord Djibril. Afterwards their comrades cheer them and Shinn and Lunamaria embrace.
With the last remnants of Blue Cosmos/Logos eliminated, Chairman Durandal unveils his ultimate solution to war - "the Destiny Plan". Chairman Durandal as an expert geneticist will act as the overseer and assign roles to individuals according to their genetic makeup. Everyone will then be governed by their genetic "destiny" and not by their individuality. According to Chairman Durandal, the ultimate goal is to make wars obsolete.
For the Destiny Plan to become a reality, Chairman Durandal has to defeat any nation with the capability and the resolve to challenge him. Before the battle, Durandal calls Shinn and Rey to meet in person at his mobile fortress Messiah. When they arrive, Durandal tells Shinn about his goals and that the ones they are fighting now are remnants of Logos, however Durandal is lying to Shinn when the ones they are fighting are actual Orb forces. Shinn hesitates about putting his full support behind the Destiny Plan. After some convincing arguments from Rey, Shinn agrees. After all the pain Shinn has endured and wanting an end to the war, the Destiny Plan is the only answer to humanity's problems that makes sense to him.
A ferocious and furious battle starts near the location of the Requiem cannon on the Moon. The Impulse, piloted by Lunamaria, tries to stop the Infinite Justice, piloted by Athrun. Seeing Athrun fighting Lunamaria, an enraged Shinn attacks Athrun, then goes into SEED mode. After realizing the terrible mistakes being made by both Shinn and herself, as she witnesses the heated argument between Shinn and Athrun, Lunamaria interposes herself between the two, begging them to stop fighting, which has Shinn hallucinate visions of Mayu, Stella and the Freedom bewilderingly. As Shinn charges madly at a shocked Lunamaria for the kill, Athrun goes into SEED mode as well, saves Lunamaria from Shinn, and cripples the Destiny, which crashes onto the Moon's surface.
While he's unconscious, Shinn has a vision of Stella, in which she tells him that she's finally got her past and thus very happy, and bidden him to see each other in the future. When he awakes with Lunamaria holding and watching over him, he then starts to cry with Lunamaria, after realizing that he was being used by both the Chairman and Rey, as well as the fact that he could have hurt and even killed Lunamaria unknowingly. He and Lunamaria then watch the Requiem explode and the Messiah crash into the moon.