In 1973, alien invaders known as BETA nearly drove mankind to extinction. In response to this unstoppable threat, large humanoid arms called Tactical Surface Fighters were developed and deployed across the globe. After 30 years, the war continues with no end in sight, until the UN proposes a joint development program between Japan and the U.S.: The Prominence Project. Yui Takamura and Yuya Bridges, two pilots who have never met, soon find themselves recruited to take part in a new age of battle.
Yui and friends are going to school to one day learn to pilot Tactical Surface Fighters against a BETA invasion. Will they be ready when that day comes?
It's trial by fire as the girls must go into battle before they're totally trained. BETA have invaded from Mars and the girls might be in over their heads as they try to protect Kyoto from such evil beasts.
Earth has been hit hard by the BETA invasion. All the best pilots from all over the world meet at a new base in Yukon, Alaska, to start a new mission - Argos Flight Team (Case 47). Training starts immediately.
Tension runs high as Yuuya, a new American test pilot at the Yukon base, confronts Yui - and his own troubled past - to pilot a Japanese Tactical Surface Fighter and complete his first mission.
Having trouble mastering the Japanese Tactical Surface Fighter, Yui tries to console and give advice to Yuuya. As Argos Flight Team goes into their next exercise, Yuuya takes Yui’s advice to heart and learns a valuable lesson.
The Argos Flight Team heads to the West Indies for some much-needed rest and relaxation. Yuuya comes to the rescue when Cryska faints during a paddleboat race. They all end up being stranded on an island, where he discovers some interesting news.
Trapped on an island with bad weather and no provisions, Yuuya, Yui, and Cryska try to stay safe the confines of a small cave. There, they must confront difference before help arrives.
Yuuya is asked to man a new weapon and must protect it with his life. Yui and Yuuya are getting closer, but how does he feel about Cryska or Inia? He comes to Inia's rescue after she is attacked by angry pilots that are upset about her origin.
Yuuya finally is going into his first real battle against the BETA, and practically everything that can go wrong does. Will Yuuya's new weapon be enough to handle such an attack?
A party is thrown to celebrate Yuuya's successful battle against the BETA. Of course, he can't attend because he's busy tending to his Tactical Surface Fighter. He begs Yui to get back into battle.
As a grand swarm of BETA is heading towards the Soviet Base, the Captain commands that all personnel evacuate and leave everything behind. Yui realizes that the evacuation a ploy for the Soviets to get their hands on the new weapon.
The BETA have broken through the front lines of defense and things are starting to look bleak. Stuck between a rock and a hard place, Yui decides to destroy the new weapon before it falls into the wrong hands.
Yuuya comes to the rescue for Yui and the new weapon. He makes sure that Yui is safe before he heads back into battle. But with his Tactical Surface Fighter heavily damaged, will he be able to fight?
Yuuya’s TSF is in critical condition and unable to fly when the Zhar Battalion arrives in the nick of time to save him. Things become complicated, however, with the unexpected arrival of Laser Class BETA…
With Zhar Battalion gone and the attacking BETA exterminated, Argos flight finally enjoys a bit of peace. This respite is threatened, however, by a new military exercise and the introduction of the mysterious Chinese lieutenant, Cui Yifei.
The mood turns tense with Yuuya’s old flight mates in town for the Blue Flag exercise. With old rivalries flaring up, will the campaign help promote camaraderie between the nations as intended, or simply serve as further fuel for their resentments?
With the Blue Flag exercises in full swing, Cryska and Lt. Cui struggle with their feelings for Yuuya. International rivalries serve as the backdrop as complicated romance and revelatory memories take center stage.
Yuuya’s troubled military past, the reason his former flight mate bears such a grudge for him, is finally revealed. Reflecting upon his past, Yuuya begins to come to terms with how he has grown as a person since joining Argos flight.
With rivalries intensifying between the nations participating in Blue Flag, the brass decide to send the Eishi on a backpacking trip through the wilderness. Romantic jealousies and a hot spring ensure that this will be a steamy outing!
As Argos prepare for their upcoming Blue Flag match, the base is infiltrated by an unknown entity. The invaders massacre the majority of military personnel and cut all communications. As friends turn on friends, Yuuya must take action.
The Refugee Liberation Front continue their takeover as Yuuya and the other uncaptured test pilots attempt to get to their TSFs and reclaim control of the base. Meanwhile, lieutenants Sandek and Dogulu plan to counter the invaders.
Yuuya volunteers to take on the 24 TSFs that the RLF stole, and, with the help of Inia, manages to fight them off. The sudden appearance of BETA and the devastating revelation of America’s secret contingency plan set the stage for Muv Luv’s climax.
Refueled and restocked, the remaining Eishi attempt to restore communication and warn the US of the BETA invasion. Meanwhile, Major Christopher and Lieutenant Sandek begin initiating plans of their own…
Christopher activates a mysterious device to try and manipulate the Scarlet Twins, but his plans go horribly wrong. With Inia and Cryska in a berserk trance and the BETA invasion imminent, will Yuuya be able to save the base?