Set in an all new Gundam timeline, the story of Iron-Blooded Orphans starts three hundred years after an event called the Calamity War between Earth and Mars. Humanity has since terraformed Mars but many of the now indigenous population want independence from Earth. It’s here our protagonists Mikazuki Augus and Orga Itsuka come in. Part of a private security firm called CGS, Orga wants to break free and secure Martian independence but a terrorist group Gjallarhorn has other ideas. It’s here where Mikazuki makes the choice to pilot the ancient Gundam Barbatos and potentially help his friend Orga and Mars as a whole.
Orga and the other Tekkadan members have finally reached Edmonton, but they are attacked by Gjallarhorn, which seeks to prevent Makanai from making it to the parliamentary session.
During preparations to depart for Edmonton, Tekkadan finds itself under attack by Gjallarhorn. Setting a trap for their relentless pursuers, Orga makes a counterattack.
With its path blocked by Gjallarhorn's fleet, Tekkadan attempts to descend to Earth in response to Kudelia's request. The battle against Gjallarhorn soon becomes very fierce.
As the fierce battle between Tekkadan and Gjallarhorn continues, a new threat appears. To protect Kudelia and the others, Mikazuki must confront it alone.
As Tekkadan heads for Edmonton, it finds Carta blocking the way, seeking a showdown. However, Mikazuki and the others won't let their progress be halted, and they press on ahead.
Kudelia and Tekkadan witness Gjallarhorn's brutal suppression of the workers. Seeing the true situation of the colonies, Kudelia makes a fateful decision.
Knowing that the Brewers are hot on their trail, the Isaribi and Hammerheads decide to take the initiative and lay a trap for their pursuers while passing by a debris field. In the ensuing battle, they successfully incapacitate the enemy. Meanwhile, Akihiro attempts to persuade his brother Masahiro to defect from the enemy side. However no avail due to the latter's melancholy, and with a death as result.
Tekkadan prepare to escort Kudelia to Earth with help from the Orcus Company. However, the route is leaked to Cora and the transport ship is ambushed by Gjallarhorn forces. Which results in the first outer space battle for Mikazuki and Barbatos.
The colony workers have launched a protest movement against the company that employs them. As they grow more radical, the situation finally develops to the point of a Gjallarhorn intervention. Before she knows it, Kudelia has been drawn into the heart of the uprising.
The orphans are pursued by Maruba, their former employer, who demands the return of his ship.
With Tekkadan and the Turbines emerging victorious over the Brewers, the survivors deal with their wounds and the death of their comrades. Meanwhile, Orga claims the Brewers' remaining mobile suits and one assault ship from Brooke Kabayan at gunpoint. The remaining Human Debris from Brewers are taken in by Tekkadan with assurances they will be taken care of on Mars. To reconcile with their feelings over the death of their comrades, Tekkadan conduct a funeral in memory of those who fell in battle before proceeding as planned.
The Isaribi and Hammerhead encounter the mercenaries known as the "Brewers".
Though Tekkadan is exhausted by its repeated battles with Gjallarhorn, its members are still determined to get to Edmonton, and they hasten toward their goal.
Third Corps instigates a mutiny that expels majority of First Corps from the CGS base. As they try to figure out how to support themselves financially, Crank returns to the base to issue a challenge to the Gundam Barbatos in order to retrieve Kudelia and the captured Graze.
Tekkadan has finally made it to Earth, successfully introducing Kudelia to Arbrau's representative, Makanai Togonosuke. However, they will have to accompany Makanai to a parliamentary general session taking place in Edmonton.
After overcoming many difficulties, Tekkadan is finally about to reach Earth. Its members head for the Dort colony cluster, to deliver an item that Teiwaz asked them to transport when they were aboard the Saisei.
The adults of CGS flee in the face of Gjallarhorn's attack, using Mikazuki and the other children as decoys. Gathering the children who have been left behind, Orga decides to fight back against Gjallarhorn, and puts a certain plan into motion.
With no one to trust after Orcus' betrayal, the Isaribi crew plan to reach out to Teiwaz, a Jupiter-based conglomerate, to guide them to Earth.
Tekkadan's members attempt to leave the colonies behind and descend to Earth at last, but they miss their chance due to one last item of business in the colonies. They are contacted by someone who claims to be their supporter.
Biscuit reunites with his elder brother Savarin, but he and Atra are quickly nabbed by Gjallarhorn forces while Atra fakes her identity as Kudelia. As Atra is being beaten by her interrogators, Mikazuki, Orga, and the rest of Tekkadan race to rescue them. Meanwhile, Kudelia and Fumitan meet a masked man who reveals the true motives of those backing their trip to the Dort Colonies.
The skirmish between Tekkadan and the Turbines comes to an end when Orga and his team raid the Hammerhead and negotiate for Teiwaz to assist them in escorting Kudelia to Earth.
Tekkadan and the Turbines arrive at Saisei to begin negotiations with McMurdo Barriston, leader of Teiwaz.
Members of Tekkadan receive video messages from their loved ones back on Mars. Meanwhile, the Isaribi is assigned a liaison from Teiwaz to oversee the vessel's activities during the long journey to Earth.
Mikazuki belongs to the private security company CGS, at the Martian city of Chryse, which has been hired to escort a girl named Kudelia to Earth. But just as preparations for departure are underway, Gjallarhorn attacks CGS in an attempt on Kudelia's life.
Tekkadan plan their route to smuggle Kudelia to Earth without alerting Gjallarhorn forces. Meanwhile, McGillis and Gaelio arrive on Mars to investigate the recent battles and encounter Mikazuki and Biscuit on a cornfield.
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