2014, fifteen years after a war between Earth and Mars. Desiring peace, Princess Asseylum of Mars holds a goodwill parade on Earth. Slaine a boy originally from Earth prays for her safety Meanwhile, on Earth, high school student Inaho and his friends receive pilot training in combat robots called Kataphraktos.

The Landing Castles of the Mars Knights that have landed on Earth launched an attack using Kataphraktos with the aim of invading the planet. The United Forces of Earth launch a counteroffensive. As the fierce battle rages on, Inaho encounters a mysterious girl.

To complete his plan, the Mars Knight relentlessly pursues Inaho and the others. Inaho is suspicious about the manner in which that knight fights. With backing from Marito’s group, Inaho begins a counteroffensive. Meanwhile, Slaine, unaware of the truth, has been ordered to provide support for the Mars Knight and is out in the field with him.

Slain has misgivings about the war. However, he has no allies around him and no way of telling who the enemy is. Meanwhile, Inaho is entrusted with a secret request by Seylum as Rayet, who is hiding her own true identity, is on edge.

Rayregalia, ruler of Mars, orders that an investigation be conducted on Earth. Slaine takes advantage of this opportunity to speak with the Martian emperor in person. Elsewhere, the assault landing ship that Inaho and the others are aboard has been sailing on a course to reach United Earth HQ.

There were no traces of the battle that once occurred on Tanegashima, which was heavily damaged in Heaven’s Fall. When they arrive, Marito is flooded with memories of the fierce fighting there. But then, the Kataphraktos of a female Mars Knight comes at them relentlessly. Meanwhile, Slain, who has been acting without the knowledge of his superiors, acts recklessly.

Inaho and the others are hard pressed in their fight against the Martian Kataphraktos. But then a mysterious fighter craft appears and joins the battle. Elsewhere, Darzana and her crew hide the damaged assault ship in a dock, and there, they discover a combat mecha of unknown origin.

Slaine is interrogated under the assumption that he knows something. Slaine manages to keep silent and not reveal the truth, thinking back to the time he once spent with Princess Asseylum. Meanwhile, Count Saazbaum seems to have ulterior motives of some sort.

Inko and the others undergo piloting training in a Kataphraktos combat simulator. Inside, Rayet reflects on her hatred, anger, and fear towards the Mars Knights, as well as her own circumstances. Yagarai and Marito also use the simulator to recreate a past battle. And the truth of what happened on Tanegashima is revealed.

Count Saazbaum launches his attack. The UEF meets its offensive in this land of brutal cold. Inaho and the others put together a plan to fight back. Working on his own, Slaine makes his way through the intense fighting to reach the Deucalion.

While Inaho and the others are carrying out their plan, they encounter Count Saazbaum’s Kataphraktos. Slaine, who had been trying to catch up to Princess Asseylum, finds himself in an unexpected situation. The fierce battle on the snowy field builds in intensity, and then—

2016, a year and a half after the assassination of Princess Asseylum. Slaine, who has earned the status of Mars Knight in spite of being an Earthborn is now served by his own personal subordinate and has been taking part in battles against the UEF. Elsewhere, the Deucalion is finishing up repairs in order to proceed to a new battlefront. One after another, the ship’s former crew returns.

At the Vers Empire’s frontline stronghold in Earthspace, Slaine leaves for their base on Marineros Island accompanied by the Stygis Squadron, compound Kataphraktoi. Meanwhile, the Deucalion arrives at the United Forces of Earth’s Trident Base, but some of the soldiers there are not fond of a unit that is equipped with Aldnoah.

The Mars Knights have assembled at Marineros Island. Slaine tries to take part in the battle, but he is looked down upon by his erstwhile fellow knights because he was born on Earth. Elsewhere, the crew of the Deucalion prepares for battle at Trident Base. Learning of the existence of Slaine’s swift Tharsis, they are wary of its capabilities.

Lt. Marito, who is serving with Yuki Kaizuka, receives orders for a new operation. Yagarai is concerned about the position this will put Yuki in, who has been assigned to a unit away from the Deucalion. Meanwhile, a group of Mars Knights who oppose the Earthborn Slaine’s rise to power plan a new attack on Earth in hopes of securing more power of their own.

Irritated by Slaine’s actions, Count Marylcian works out a new strategy with Count Barouhcruz. Elsewhere, Rayet loses her composure in front of the Mars Knight prisoner, and Inaho deduces her true intentions. Meanwhile, Slaine talks about birds with Eddelrittuo.

Princess Lemrina is distraught over an unexpected situation, but Slaine tells her that on the contrary, he will use it to his advantage. But deep down, he gradually feels more and more cornered. Elsewhere, the Deucalion’s crew links up with a UFE company that is engaging a powerful enemy. Then, on the front line, Inaho gets out of his Kataphraktos.

The Orbital Knights rally under Princess Asseylum’s new proclamation with renewed determination. Slaine launches a new operation, partly to contain the factions who are against him. Elsewhere, Capt. Magbaredge, who has been summoned by senior UFE officials, realizes just what they think of the Deucalion. There, she receives orders for a new mission.

The UFE is overwhelmed by the Mars Knights’ advance. Inaho and the Deucalion take part in the fighting, but they find themselves hard pressed by an unexpected attack. Elsewhere, Slaine unburdens himself to Eddelrittuo. A Mars Knight who requested an audience with Princess Asseylum did so with an ulterior motive.

Under orders from United Forces of Earth’s General Headquarters, the Deucalion and her crew take part in an assault mission. They formulate a plan that will let them fight the Mars Knights. Elsewhere, with fresh determination, Slaine advances his invasion of the surface to broaden his power base. However, there are those who have doubts about his true motives.

The Deucalion receives new orders, but Capt. Magbaredge senses that another mission is in motion behind the scenes. Inaho takes action to protect Princess Asseylum. Elsewhere, Slaine explains his intentions to Princess Lemrina. He does not know that the situation is changing…

Inaho and the crew of the Deucalion steel themselves for the final battle. Capt. Magbaredge confronts Vice Admiral Hakkinen and takes part in the dangerous mission. Meanwhile, Slaine is determined to commit all his forces to prepare for a final showdown. Princess Asseylum, having been rescued, resolves to confront their fate.

The war has come to one final battle. Having reached an understanding, Slaine resigns himself to his fate. Elsewhere, Inaho answers the call of his own destiny. There is someone who sheds tears at the sight of the battlefield where all too many lights flare, then die out. A solitary girl saw the final moments of their battle.