A colonized space had finally achieved peace, until a mysterious enemy, the UE, enters the scene and attacks colonies and other targets. Our main protagonist is from a destroyed colony, safely living on another. Before fleeing and surviving the attack however, he is entrusted with a data package which contains the one hope for humans to stand up against this powerful foe, plans for a Gundam. Flit Asuno has spent most of his years on this peaceful colony studying science and realizing the plans, cultivating in the production of one. One which Flit ends up piloting himself when his new home is threatened.
Federation ace pilot Woolf Enneacle wakes up from healing sleep aboard the Diva. He tries to claim the Gundam for himself to Flit's chagrin, and decides to have a mock battle to determine who should pilot the mobile suit. However, during the mock battle, the two of them are suddenly attacked by the UE, and end up making a startling discovery about how the UE are able to remain hidden.
The Diva flies at low altitude to avoid enemy detection while passing through a desert, when it is ambushed by the "Phantom 3", a Vagan special unit whose desert-oriented gear gives them the upper hand. Kio and the others struggle to keep the enemy at bay long enough for the Age Builder to complete their newest weapon, the G-Hopper, and dispatch it to assemble the Gundam AGE-3 Fortress.
The U.E. attack of Nora has left the colony in imminent collapse. The Federation commander of the colony, Hendrick Bruzar, came up with a plan to use the flagship battleship, Diva, to save the colony core, thereby enabling the colony inhabitants to escape the destruction. However, the captain of the Diva has other plans. Meanwhile, Flit tries to escape the colony while piloting the Gundam, but comes upon a stranded girl named Yurin, who seems to have mysterious powers of her own.
On their way to the Federation base of Roustroulam, the crew of Diva learns that one of their pilots Shanalua Mullen is a spy working for the Vagans. Kio is ordered by his grandfather to help defend the base against the Vagans, but he decides to go after Shanalua instead, wondering about the reasons behind her treason.
The Battle of Roustroulam continues, but when Flit and the others realize the Vagans' true intentions, they must race against time to disarm the bombs left behind by the enemy.
The Diva leaves for lunar orbit; they are attacked by pirates along the way.
The crew of Diva takes heed of the message left behind by Asemu revealing the existence of EXA-DB, an ancient military database whose secrets can change the course of the war. Zeheart joins fellow commander Zanald Beyhard in a pincer attack on the Diva, and to protect it from the enemy, Kio pilots the brand new Gundam AGE-3 Orbital.
At Vagan's capital, Kio is brought before their leader Fezarl Ezelcant, who treats him more like a guest than a prisoner. Ezelcant has Kio explore the colony to learn about the harsh situation of its people while Zanald's crew have the Gundam AGE-3 analyzed as part of their plans to develop their own Gundam.
Kio helps Ezelcant to complete his own Gundam in exchange for medicine for his new friend Lu. He then spends his days at Vagan happily besides Lu and her brother Deen until the Visidians infiltrate the colony to rescue him and retrieve the Gundam AGE-3.
After a brief reunion with his family, Kio takes part in a mission to recapture the Federation Lunar base from the Vagans while determined to follow his will to protect everyone, regardless of side, piloting the AGE System's ultimate creation, the Gundam AGE-FX.
Kio's confront with Fram in interrupted by Girard Spriggan, a former member of the Earth Federation who switched sides. As Kio struggles against Girard, her past and the reasons for her defection are revealed and Flit joins the battle with his upgraded Gundam AGE-1 Gransa to assist him.
The Federal Forces break the enemy's defense lines and infiltrate the Lunar base. While Seric Abis convinces the Vagans to admit defeat, Girard's X-Rounder powers go berserk and she starts attacking both allies and foes alike.
Having successfully taken over the Lunar Base, the Federation Forces turn their attentions to La Gramis, the Vagan's main fortress. Kio and Asemu confronts Flit about his urge to take revenge on the entire Vagan race for all the friends and loved ones he lost during the war and after revealing to Zeheart all the truth about Project Eden, Ezelcant nominates him his sucessor, entrusting him with the Gundam Legilis.
Zeheart confronts the mobile armor SID determined to master the full power of the Gundam Legilis and reclaim the EXA-DB. The Bisidian take heed of the battle and also launch an attack against SID, but it proves more powerful than Asemu and Zeheart can handle until they end up joining forces to defeat it.
The Vagans carry out large-scale invasion plans using the Second Moon of the Vagans', La Gramis. The Federation, knowing they must put a stop to those plans, mounts an operation to capture La Gramis. We follow both sides as the soldiers ready themselves for the final battle. What does the future hold in store for this ultimate battle?
Within the pitched battle for La Gramis, Kio finds he's fighting Deen, a Vagan he had previously befriended. For Kio, the attack by the X-Rounder-power-enhanced Deen is the worst enemy he could possibly face.
Zeheart knows that if the Dig-Magellan were to fire, it would kill many of his comrades, but steeling his heart, he gives the command to fire. Flit, having predicted the attack and the destruction of Diva works to save Gundam and the Diva's crew. If that attack fails, Zeheart will be driven from the Vagan forces, and what will Asemu do…?
The siege of the Space Fortress La Gramis grinds into its final stages, and despite the tremendous losses to both the Vagan and Federation sides, the atrocities of war only seem to be on the increase. As the long struggle reaches its end, can Flit, Asemu and Kio reach any kind of agreement with Ezelcant?
The battle for the Lunar base intensifies as Zeheart and his aide Fram Nara set for the frontlines. Kio attempts to dissuade Fram without success and just when he finds himself in a pinch, Asemu joins the fight and confronts Zeheart about Ezelcant's true intentions.
Just after the birth of his son Kio, Asemu leaves for a special mission but never returns. On A.G. 164, the Vagans launch a large scale invasion on Earth that overruns the Federation Forces by surprise. Just when everything seems lost, Flit and Kio board the brand new Gundam AGE-3 to fight back.
Diva was preparing to pull Nora's Core when two new UE approached them so Grudeck decided to confront them first before resuming the operation. The new UEs proved to be a formidable opponent to Flit who started losing his temper but Yurin calmed him down while helping him come up with a plan to effectively take down their opponent. One of the two UEs entered Nora and attacked the control base where Bruzar was located, badly injuring him in the process. Flit is fighting the remaining UE to distract him away from Diva, but when the DOTS rifle's ammo was depleted he stopped the UE by shielding the Gundam in front of Nora and told the UE that he won't let the citizens harmed. To his surprise the UE left. Diva was about to pull the Nora's Core when an large metal debris hindered the core from moving, so Bruzar sacrifices himself by piloting an MS carrying explosives to blow up the debris hindering the core, leaving his hope to Flit and the crew of Diva, Afterwards, Nora was completely destroyed but the core was saved and Diva crew mourning the loss of Bruzar, Flit and Yurin parted but not without Yurin giving her ribbon to Flit in hopes that they'll meet again.
Diva docks at the space colony Fardain. The Federation planned on arresting Grodek and having him court-martialed but he managed to blackmail the officer in charge. There Flit meets a young boy who steals the Gundam and attacks several UE mobile suit type forces with it. The boy then returns the Gundam back to Flit and leaves. In another section of Fardain the boy is met by several hooded men who explain that he is a part of the group of people "chosen by Eden".
Flit, imprisoned by Zalam for the destruction he wreaked, is brought before their leader Don Boyage. Flit argues that Zalam and Euba should cease their feud over control of Fardain, but is rejected by Boyage. Then, Euba's boss Ract Elfamel attacks at the lead of a mobile suit squadron. Another war breaks out within the colony. Flit stands forth in the Gundam to prevent it, but a U.E. assault sparks a three-sided battle. Unable to use beam weapons inside a colony, the Gundam takes on a new form to stand up to the U.E.
To take down the U.E. that have infiltrated Fardain, Flit fights in the Gundam's new form: Titus. What the Titus loses by abandoning its Dodds rifle, unusable in colonies, it more than makes up for in brute force. Meanwhile, doubts remain between Zalam and Euba, and clashes erupt as they come together on the battlefield. As the situation becomes more desperate, Flit fights to unite the clashing Zalam and Euba elements under one banner. A new mobile suit rises on the battlefield. Who pilots its alabaster form?
Flit questions Woolf about the source of the new G-EXES. Woolf confesses and leads Flit to his old haunt, the Madorna Factory. Flit is amazed by the range of mobile suits under construction. But then, a shocking sight! Among the other models is a U.E. mobile suit! Flit and company are astounded. Just then, the U.E. suit activates and begins to destroy the contents of the factory. Flit and Woolf fight together against it, but cannot resist its fierce attacks...