On April 19th, 1973, a race of extra-terrestrial lifeforms launched a landing unit from the moon, which touched down on Earth, in central Asia. Ever since, mankind has been engaged in a losing war against this alien species, known as the BETA, as they have gradually expanded outwards across the globe. After 20 years of non-stop fighting, the war has reached the shores of Japan...

Shirogane Takeru found himself inexplicably transported to a world that resembled his own in many ways, with one major difference: For nearly 30 years, mankind has been at war with the alien BETA, who have succeeded at wiping out over half of humanity and had nearly captured the entire Eurasian continent. As Takeru tried to come to grips with this bizarre new reality, he realized too late that the majority of humanity will be abandoned with the Earth, as the chosen few escape to the stars, hoping to find sanctuary. Now, equally inexplicable reasons, he finds himself returned to the first day of his time in this alternate world. Will the experiences and knowledge he has gained allow him to make a difference?

As Takeru starts to feel anxious about whether or not he can actually make a difference, Professor Kouzuki demands more concrete evidence of his knowledge about future events.

Takeru's efforts to change the future are starting to have an effect, as the 207th's Tactical Surface Fighters show up earlier than in the previous timeline. And if an idea he's cooking up works, it might make them even more effective weapons against the BETA.

Takeru and Professor Kouzuki have collaborated to create a new operating system for the 207th's Tactical Surface Fighters, making the anti-BETA weapons more maneuverable and responsive than ever. But will it even matter if Yuuko can't actually make some progress on the mysterious Alternative IV plan?

In order to help Professor Kouzuki fulfil her plans for Alternative IV, Takeru partakes in an experiment designed to send him back to his home world.

Takeru's trip back to his original world concludes after an encounter with his childhood friend, Sumika. After his return, he learns about the enigmatic Yashiro Kasumi's mysterious past.

An insurrection threatens to ignite a full-scale civil war in Japan, and the 207th Tactical Armored Flight finds their first combat mission might be against other humans, instead of the invading BETA aliens.

Takeru and his training squad head out to assist the UN and Japanese forces in dealing with a coup d'état, but they find themselves dealing with what might be the most vital mission in the entire conflict.

As Takeru and the 207th Training Flight escort the Shogun across Japan, Professor Yuuko's personal task force fights a desperate battle to keep the rebels off their tails.

The Shogun and her escorts have been surrounded by the rebels, who have offered them a 60 minute ceasefire in the hopes of a peaceful resolution. Can Takeru, the 207th Training Flight, the Royal Guard, and the US Army find a way past them to return to Yokohama Base?

Negotiations have fallen apart, as the rebels renew their attacks on the assembled UN-US-Royal Guard forces. Will the 207th Training Flight make it back to Yokohama Base alive? And will Takeru be able to save the world by helping Alternative IV become a reality?

Takeru visits the peaceful world he originally came from to recover the research necessary for Alternative IV to be a success. Upon his return to the war-torn world ravaged by the BETA, he discovers a surprise that brings him one step closer to victory... and danger.

A new set of trials testing the combat readiness of Takeru's XM3 operating system takes a turn for the dangerous.

After a soul-shaking brush with tragedy, Takeru decides to return to his home world.

With it now obvious that he's having unexpected effects on his peaceful home world, Takeru has to make a tough decision.

Takeru returns to the world ravaged by the BETA, only to be shocked when Professor Kouzuki introduces him to 00 Unit.

As Takeru grapples with the truth about the 00 Unit, a deadline to get it functional looms.

The A-01 Squad find that they will be part of a joint operation between the UN and Japan to attack the BETA hive on Sadogashima.

The mission to retake Sadogashima is underway, and the Valkyries take to the battlefield.

The Susano-O arrives, and the outcome of Operation 21st will depend on the performance of the flying fortress.

With the Susano-O inoperable, the Valkyries move to recover the 00-Unit as BETA continue to swarm Sadogashima.

A massive horde of BETA surfaces from beneath Sadogashima, putting the A-01 Task Force and success of Operation 21st in danger.