This Original Net Animation (ONA), four parts series, takes place concurrently with Mobile Suit Gundam, during the One Year War. In UC 0079, the Federation and Zeon troops engage in a fierce battle in the "Thunderbolt Sector", a shoal zone littered with debris from destroyed space colonies, named for the frequent electrical discharges. The story focuses on Federation soldier Io Flemming as he battles Zeon's best sniper, Daryl Lorenz.
With both sides suffering massive casualties, the Full Armor Gundam engages in a final showdown with the Psycho Zaku. Meanwhile, the surviving members of the Moore Brotherhood board the Dried Fish to take it over, but the remaining members of the Living Dead Division refuse to be taken prisoner and plan to self-destruct the vessel along with everyone on board.
The Moore Brotherhood's Beehive flagship launches a squadron of GMs across the Thunderbolt Sector to break through the Principality of Zeon's defenses, only to be shot down by the Living Dead Divison and their Big Gun units. Io Fleming, who manages to eject from his GM, guns down a Rick Dom pilot before commandeering the mobile suit and returning to the Beehive with the sniper location data. He is then assigned to pilot the new Full Armor Gundam prototype, which he uses to flush out three Big Gun units. Living Dead Division ace sniper Daryl Lorenz vows to avenge his fallen comrades and kill Io.
During the Full Armor Gundam's second sortie in the Thunderbolt Sector, Io once again confronts Daryl. Daryl narrowly escapes after throwing a Cracker grenade at the Gundam, but he loses his left hand in the process. As the Living Dead Division is desperate to hasten the Reuse P. Device project to combat the Gundam, Daryl has his right hand amputated so that his body will have full control of the experimental Psycho Zaku.
The Moore Brotherhood receives reinforcements from the Earth Federation, but the new mobile suit pilots are young teenagers, much to Io's chagrin. Feeling the pressure of the war, Claudia resorts to drugs before Io snaps her out of an overdose. Io leads the young cadets to break through the Living Dead Division's final defenses, but the battle becomes a massacre due to the young pilots' inexperience.
During the Earth Federation's assault on the Zeon's A Baoa Qu fortress, Io and his comrades escape captivity while several Zeon forces retreat, taking Io's Gundam with them. Eight months after the end of the One Year War, the Federation continues to battle Zeon remnants on Earth. The Federation carrier Spartan enters Earth orbit, but a Musai-class ship launches its Komusai shuttle for a kamikaze run on it. Suddenly, a new Gundam piloted by Io is launched from below and it slices the Komusai in half to save the Spartan.
The South Seas Alliance, a Buddhist radical cult faction of the Federation, plots to declare itself independent. Furthermore, it is discovered that they possess the Reuse P. Device technology of Daryl's Psycho Zaku. The Spartan is assigned to track and destroy the Psycho Zaku before the South Seas Alliance can mass-produce the technology. In Antarctica, Bianca's squadron is ambushed by Zeon mobile suits. Io sorties in the Atlas Gundam and dispatches the enemy units before facing a Grublo mobile armor. The battle sends both units far too deep underwater and Io with his equipment lost slowly sinks to the bottom of the sea, but Bianca in her damaged Guncannon Aqua lifts him back to the surface.
Due to the emotional trauma Karla suffered during the One Year War, her mind has regressed back to that of an adolescent child with the Zeon Remnants now trying to take care of her in hopes of her adult mind to recover. Daryl's Acguy squadron heads to a South Seas Alliance-controlled city in Southeast Asia to retrieve a spy, but their cover is blown and they must fend off against the island's mobile Suits. Meanwhile, the Spartan is confronted by a South Seas Alliance mobile suit Squadron, with Io's former commander and lover Claudia leading them.
Having entered the jungle, the Acguy team finds itself in a fierce battle with the South Seas Alliance's Dahle forces. Refusing to abandon his mission of contacting the spy, Daryl is backed into a corner. Meanwhile, the South Seas Alliance's border garrison has deployed Goufs and Do-dais to block the Spartan's path. As they resort to suicide attacks in an attempt to break into the ship, what are they trying to achieve? In order to confirm the identity of the garrison commander, who gives her name as Claudia Peer, Io boards a GM Ground Type-C and fights together with Bianca's Corvette Booster. Intercepting the Goufs and Do-dais, they take them down one by one. The three-way fighting continues to intensify, in the dense jungle and at high altitude...