Cagalli is the winner in the 56th Gundam National Census voting (held between 7/28/2008 and 8/3/2008) for the question: "Summer swimming suits! In Gundam Seed or Gundam Seed Destiny, which female character will you like to see in a swimming suit?"
While Kira is a Coordinator (a person who is genetically-altered), Cagalli is a Natural. In the Cosmic Era time line, she seems to be the only Natural who can go into SEED Mode.
Cagalli reunites with Kira, now a pilot for the Archangel, a warship of the Earth Alliance Forces. At the Desert Dawn's frontline base, Mu La Flaga asks for the formal name of the "Goddess of Victory", and Sahib Ashman unwillingly replies "Cagalli Yula." After ZAFT BuCUEs under the command of Andrew Waltfeld destroy the town of Tassil, Cagalli and several other members of the Desert Dawn chase them. Outmatched, several resistance fighters, including Cagalli's friend Ahmed El-Fasi, are killed. (In the novelisation of Gundam SEED, Cagalli suggests the chase in the first place.) Ledonir Kisaka manages to protect Cagalli until Kira arrives. She and Kira quarrel over her actions, ending with Kira slapping her across the face. Cagalli is later bequeathed a green stone by Ahmed, who had unrequited romantic feelings towards her.
In episode 19, Cagalli and Kira are sent to gather supplies, but are accidentally caught up in an attempt on the life of their adversary, Andrew Waltfeld, the Desert Tiger, by Blue Cosmos terrorists. Andrew knocks Kira and Cagalli prone to protect them, and Kira keeps one of the terrorists from shooting Andrew thowing a gun at the terrorist and then kicking him.
Andy brings Kira and Cagalli to his headquarters. Though they want to leave, he wants to thank them. Andy's girlfriend Aisha takes Cagalli away to be cleaned up, which is retconned into a shower scene that contains fanservice in Gundam SEED: Special Edition.
Andrew has a conversation with Kira until Aisha brings in Cagalli in an elegant dress, Kira and Cagalli quarrel, which the adults find humorous.
Andrew then reveals he knows Kira is with the Earth Alliance Forces. He points a gun at Kira and Cagalli and asks how the war will end, if it will be after all enemies are dead. He also says he does not know why Kira, a Coordinator, is fighting his own kind, but as long as he pilots the GAT-X105 Strike, they are enemies. Andrew then lets them go, since Kira has previously saved his life. In this encounter with Andrew, Cagalli learns Kira is a Coordinator.
In a battle between the ZAFT forces, lead by Andrew, and the Archangel with the aide of the Desert Dawn, Cagalli commandeers a spare FX-550 Skygrasper. She is shot down but lands safely and the ZAFT forces retreat.
After the battle, the Archangel leaves Africa, heading for Orb. Cagalli and Ledonir accompany them. While traveling on the Indian Ocean, she comforts Kira, who is upset about the deaths of people he failed to protect, and Andrew, the first person he killed who he knew personally. Kira's girlfriend, Flay Allster is clearly jealous of Cagalli's closeness to Kira.
Over the Indian Ocean, Cagalli chooses to pilot a Skygrasper once again, aiding the Archangel in battle against ZAFT forces. Cagalli is shot down, but not before shooting down a transport carrying Athrun Zala and his mobile suit.
Both end up marooned on the same island, where Athrun takes her prisoner. They discuss the war and their differing views. Later, both are retrieved by their respective sides, with neither revealing the other was present.
In episode 25, the Archangel with Cagalli on-board, reaches Orb, though for political reasons the country claims the ship was driven off. When the Archangel enters Orb territory, she reveals that she is Cagalli Yula Athha, the daughter of the Orb Union's Chief Representative Uzumi Nara Athha. She is clearly upset with Orb's secret weapons development on Heliopolis and blames her father. She tries to help Kira by reuniting him with his family, but he refuses to see them. Cagalli's concern over Kira culminates in her embracing him just before he leaves Orb with the Archangel, telling him not to die and to come back to see her again. These actions clearly distress her father and his parents.
Athrun regains consciousness on the Orb transport ship, where Cagalli points a gun at him and demands to know what happened to Kira. Athrun is upset about killing his friend, but justifies it by saying Kira had killed several ZAFT comrades, ending with his friend Nicol Amalfi's death. Cagalli repeats her father's teachings, saying that killing for vengeance will never bring peace but simply more conflict. Both are reduced to tears.
Before releasing him back to ZAFT, Cagalli gives Athrun a red stone pendant sacred to Haumea (the goddess of fertility and childbirth worshipped in Orb), and says she does not want anybody else to die.
In episode 37, the Archangel returns to Orb after defecting from the Earth Alliance, with Kira, now piloting the ZGMF-X10A Freedom on board. Cagalli reacts very emotionally when she finds out Kira has survived and he recounts his side of the battle with Athrun.
In episode 38, Muruta Azrael, leader of Blue Cosmos, directs an attack on Orb, trying to force the nation to concede to the Earth Alliance. Athrun joins the fight in the ZGMF-X09A Justice. He was originally ordered to retake or destroy the Freedom, but instead he helps Kira and the others stave off the Earth Alliance. After doing so, a tearful Cagalli runs up to Kira and Athrun as they meet face-to-face and hugs them both.
This reunion is ruined when the Earth Alliance attacks again. Cagalli's father, gives her a photograph of her and Kira when they were babies - in the arms of their birth mother, Via Hibiki - and tells her that although she is leaving her father, she will not be alone, for she will be with her brother.
Cagalli then takes off onboard the Kusanagi and watches in horror as her father and other Orb leaders sacrifice their lives detonating the Kaguya mass driver to prevent the Earth Alliance from capturing it.
In the final episodes of Gundam SEED, Cagalli pilots the MBF-02 Strike Rouge as a member of the Three Ships Alliance, which is trying to stop the genocidal intentions of the leaders of both sides, Patrick Zala and Muruta Azrael.
Cagalli meets Athrun again and both notice Athrun's fiancee, Lacus Clyne getting closer to his best friend Kira Yamato. At the same time, Athrun and Cagalli begin developing feelings for one another. This is first shown when Athrun gives Cagalli a hug and apologizes to her, in episode 43. Before the Second Battle of Jachin Due, Cagalli declares that she will not let Athrun or Kira (in her words "That guy who's probably my little brother") to die and the two (Athrun and Cagalli) share a kiss.
During this final battle, Cagalli boards the ZAFT superweapon GENESIS with Athrun, arriving in the control center to find Athrun's father dying. Rather than follow his father's wish to use the weapon to destroy life on Earth, Athrun detonates his nuclear-powered Justice unit inside GENESIS, destroying it before it fired on Earth.
Cagalli follows Athrun and persuades him to vacate the Justice before it self-destructs, board the Strike Rouge and escape with her. Together, they find Kira floating in space not far from a heavily-damaged Freedom. With tears, they rescue Kira and recover the Freedom.
Although she is a Natural, Cagalli is also capable of going into SEED mode in battle like Kira and Athrun, as evidenced when she avenges the deaths of Astray pilots Asagi Caldwell and Juri Wu Nien. So far in the Cosmic Era, Cagalli is the only Natural to have gone into SEED mode.
Gundam SEED Destiny is set two years after Gundam SEED. The Bloody Valentine War ended with the Treaty of Junius Seven colony.
They remain on board while the Minerva pursues and battles the thieves. Cagalli meets Shinn Asuka a refugee from Orb who is serving with ZAFT and blames her father and his policies for the death of Shinn's family in the Bloody Valentine War. This is one of many difficult situations Cagalli is placed in as she has to struggle with her father Uzumi's legacy, her own coming of age, and her own goals and desires.
In episode 5, Athrun aids the Minerva and her mobile suit pilots in trying to stop terrorists from dropping the Junius Seven Colony on to the Earth. The Minerva and those on board land on Earth and proceed to Orb.
Cagalli and Athrun have little time together as she is busy with official duties. Athrun gives her a ring and they kiss, but he leaves for the PLANTs shortly afterwards to meet with Chairman Gilbert Durandal.
In episode 14, Kira kidnapped Cagalli from her wedding with his ZGMF-X10A Freedom and takes her to the Archangel. At first Cagalli is angry with Kira, but he reminds her about all things her father said. Upon realizing that she made a big mistake, Cagalli breaks down and cries in her brother's arms. She later assumes a bridge position, taking the communications role previously held by Miriallia Haw.
Athrun and the others disagree strongly on many points. He tells Cagalli that if she wants Orb to stop fighting against ZAFT, she needs to return to Orb and get them to end their ties to the Earth Alliance. (Cagalli eventually chooses to do this.) In return, Athrun is told that Coordinators have attempted to assassinate the real Lacus Clyne, meaning that Kira and the others do not trust Chairman Durandal. However, Athrun retorts that Kira and the others are jumping to conclusions and they do not have enough evidence to make him doubt Durandal.
While Athrun, whose wounds have reopened recovers, tended to by Meyrin Hawke Cagalli presents a global television broadcast, opposing Chairman Durindal's Destiny Plan. Cagalli is interrupted when "Lacus Clyne" pirates her broadcast. Shortly thereafter, the real Lacus reveals Gilbert Durandal's duplicity on global television.
In Gundam SEED Destiny "Final Plus", footage had been added to the scene in episode 45 where Cagalli had removed the ring Athrun gave her. The new footage shows Cagalli embracing her friends Kira, Lacus, and Athrun before they leave Earth since she stays in Orb to attend to her duties.
According to an interview with Mitsuo Fukuda, her name is derived after the Japanese word kagaribi (a watch fire or a bonfire).