The Apollo 17 mission found ancient technology known as the Hypergate on the moon that allowed humans to settle on and terraform Mars. More ancient "Aldnoah" technology found on Mars was claimed by the immigrants, who founded the Vers Empire, leading to a tense state of affairs with Earth that eventually culminated in open war breaking out in 1999. During a battle between the Earth Federation and the Vers Empire on the moon in 1999, the Hypergate went out of control and destroyed the Moon in an event that would come to be known as Heaven's Fall. 15 years after Heaven's Fall, the Princess of Vers, Asseylum Vers Allusia, goes to Earth on a peace mission despite being discouraged by Slaine. Back on Earth, terrorists attack the parade of the peace delegation, which is witnessed by Inaho and his friends. Although it initially seems that the limousine managed to avoid the terrorist attack, they manage to hit it with a second volley, and it is believed that the princess is killed. In retaliation, the Martian Vers Orbital Knights start an all out assault on Earth on their landing castles, and destroy New Orleans. Children mistake them for shooting stars and wish for world peace.

The Vers invasion begins with Landing Castles crashing into New Orleans, Maputo, Beijing, and Tokyo. Martian Kataphrakts emerge and begin to devastate the Terran defenders. In Shinawara, while preparing to evacuate, Inaho finds Edelrittuo and an unknown girl and informs them they need to evacuate. The girl subdues him and asks him what the evacuation is for, prompting Inaho to inform them about the assassination of Princess Asseylum. The girl then reveals to Inaho that Asseylum became ill after making planetfall due to the change in gravity and it was actually a body double that died. Meanwhile, the terrorists who committed the assassination are revealed to be Vers loyalists, but are promptly killed by Baron Trillram of the Vers Empire to ensure the truth about the false flag operation is never revealed. 2nd Lt. Marito's squad engages Trillram, but are defeated by him. While chasing Inaho and his friends who are escaping in an APC, Okisuke is thrown off the vehicle and disintegrated by Trillram's shield. After entering a tunnel, Inaho receives orders from Lt. Marito to draw Trillram's Kataphrakt away to buy more time for an evacuation.

Inaho and his friends find themselves holed up in the school with orders to distract the enemy Kataphrakt while 2nd Lt. Marito builds a plan to evacuate his students and the civilians with them. Not satisfied to just be a distraction, Inaho comes up with a strategy to fight back against Trillram and his seemingly impervious mech. The unknown girl and Rayet, both feeling some personal responsibility for the situation, volunteer to drive the decoy truck, and the team begins their operation. Meanwhile, Marito, backed by by Colonel Magbaredge, rallies his crew and rescues the noncombatants from Inaho's group while Inaho, Calm, and Inko engage Trillram. When Trillram finally catches the decoy truck, the unknown girl reveals her true identity as Princess Asseylum, distracting him just long enough for Inaho to strike the finishing blow. While Inaho and his comrades regroup and celebrate, Slaine and Trillram prepare to escape. Trillram reveals that the assassination of the Princess was a Martian plot all along, and that he must rearm and eliminate her as quickly as possible. In response, a shocked and enraged Slaine pulls Trillram's gun and shoots him multiple times, killing him.

The Martians bombard the Earth with meteor attacks. Inhao and friends continue to travel with a Terran military squad when they are attacked by another Martian Kataphrakt.

The Emperor of Mars calls for a cease fire. Inaho and friends take the moment to rest aboard an Earth Navy Ship. Slaine tries to find a way to reveal the conspiracy of the Martian Forces true intentions.

The Emperor of Mars broadcasts an offcial declaration of war against Earth. Inaho and his friends are drafted into the military and Slaine is on the run.

Lord Saazbaum decides to hold back on chasing Slaine, and instead tracks as he flees to Earth. Meanwhile Inaho and friends have arrived at Tanegashima, a mysterious location.

Princess Asseylum reveals herself to the Earth forces and Slaine remembers the time he spent with the Princess whilst being tortured by Count Cruhteo.

Slaine wakes up in the Landing Castle of Count Saazbaum and learns the true intentions of the Count. Rayet and Lt. Marito must deal with with their individual memories of those they have lost to the Martians.

Inaho successfully revives Asseylum in the shower room using CPR and a defibrillator, but Rayet grabs Magbaredge's pistol and holds everyone hostage. First Rayet blames Asseylum for being able to integrate into the United Earth forces while she and her father were outcasts, then she turns the gun on herself. However, Inaho disarms her, offering her another chance to fight the Martians. Magbaredge throws Rayet in the brig, then goes off to watch Marito's confession in Yagarai's lab. Meanwhile, Saazbaum reveals to Slaine that the Vers Empire convinced their people to attack the Earth to distract from their own problems of producing food and water on a relatively-dead Mars. Saazbaum and his wife, Viscountess Orleans, joined the attack on Earth at Tanegashima but Orleans was killed by Heaven's Fall as he escaped. Back on Earth, the Deucalion finally arrives at UE headquarters in Russia, and Asseylum tries to broadcast her message calling for a ceasefire. However, Saazbaum tells Slaine that the sattelite base on the Moon is staffed by his men so no Martian will hear it. Saazbaum then offers Slaine a choice: stay and fight with him, or escape to Earth and be treated as an enemy.

Count Saazbaum's Landing Castle descends down to Earth and begins an assault on the United Earth HQ. The Deucalion is under direct attack from Martian forces and Princess Asseylum must make her way to the ship.

The Deucalion has collided with Count Saazbaum's Landing Castle. Inaho, Yuki and Inko must now escort Princess Asseylum to the Aldnoah Drive. Meanwhile Slaine is rushing back to the Landing Castle and Count Saazbaum is still out there in the Dioscuria.