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.
Mikazuki's group, Tekkadan, has been commissioned to escort Kudelia on an inspection of a halfmetal mine. Under Tekkadan's protection, she completes the inspection schedule without incident. But suddenly, Tekkadan finds itself under attack by space pirates.
Despite some casualties, Tekkadan has successfully repulsed the space pirates of the Dawn Horizon Corps. It appears, however, that this enemy was just one part of a huge space pirate group, and Orga decides to counterattack in anticipation of further assaults.
Deploying all the fighting strength it possibly can, Tekkadan attempts to capture Sandoval Reuters, the leader of the Dawn Horizon Corps. During a hard fight against unequal odds, Gjallarhorn's outer lunar orbit joint fleet Arianrhod also joins the battle. A three-way free-for-all begins between Tekkadan, the Arianrhod fleet, and the Dawn Horizon Corps.
Mikazuki and Orga visit Allium, leader of the ideological group Terra Liberionis, to resolve the issues surrounding the attacks of the Dawn Horizon Corps. Meanwhile, McGillis arrives at Gjallarhorn's Martian branch, and he offers Tekkadan a certain proposal.
Tekkadan's Earth branch, which is now serving as a military advisor to Arbrau, is consumed with preparing the launch ceremony for the Arbrau Defense Forces. At Makanai's request, Tekkadan takes charge of security for the ceremony venue. But with the sound of an explosion, black smoke rises from the site.
A conflict between the rival economic blocs Arbrau and SAU breaks out as their armies clash on the Balfour Plain. Tekkadan also joins the battle under the command of Galan Mossa, but its members become exhausted as the war of attrition continues day after day.
Gjallarhorn has received a mediation request from the SAU. In order to break the prolonged stalemate, McGillis personally enters the battlefield in a mobile suit. Galan's team launches an attack on McGillis, who is whittling down Arbrau's fighting strength.
Via a certain matter on Earth, the connection between Tekkadan and McGillis grows even stronger. Meanwhile, the Gundam Vidar, which has been undergoing adjustment by the Arianrhod fleet, finally rolls out.
The awakened mobile armor, along with a huge quantity of sub-units, heads for a densely populated area to begin its attack. Tekkadan attempts to hold back the onslaught, but is helpless against its overwhelming power and superior numbers.
Outnumbered, Tekkadan turns to McGillis for assistance, and launches a mobile armor mopping-up operation. Meanwhile, a strange phenomenon occurs in the Gundam Frames that are confronting the mobile armor.
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