Shirogane Takeru wakes up three years after the end of Unlimited to find himself back in his room. Although he first thinks that everything that had happened to him was a dream, he soon feels that something is wrong, and leaves the house to find that he has been sent back in time to the beginning of the events in Unlimited. Unwilling to accept something like Alternative V, he decides to help Professor Kouzuki to complete Alternative IV and save mankind.

History

The history of this world is different from the one we know; historical alterations that diverge events from our own over time, to the discovery of life on Mars. In a way no-one would ever have wanted. First detected on the Red Planet in 1958, the organisms that would become known as Beings of the Extra-Terrestrial origin which is Adversary of human race, or BETA, would then arrive on the Moon in 1967, met by a permanent human presence by way of a space program ahead of our own at the equivalent time. Upon the Moon, it would become apparent that these aliens were hostile, humanity’s forces being driven back and eventually abandoning the Moon entirely. The BETA made planetfall on Earth in 1973, in Kashgar. By 2001, the population of the human race is down to 1 billion individuals, 1/6 of what it was when the BETA arrived.
Dismissing it as a dream, he realizes he woke up a lot earlier than before and decides to surprise Sumika. He exits his home only to find out that the world around him is now in ruins. Finding a huge, completely destroyed mech lodged into the side of his house, he becomes happier than ever. Convincing himself that it's a dream, he decides to take advantage of the situation and explore the world. When he arrives to where his school should have been, he is apprehended by guards outside the gate, and is thrown into jail. He is freed by Kouzuki Yuuko, whom he recognizes as his teacher, but in reality is the vice-commander of the United Nations 11th Force's Yokohama Base. There, he finds out about the terrible truth of the state of the world: a race of aliens, the BETA, have invaded Earth and have been fighting against humanity for decades, destroying many nations in the process. Even though he is still skeptical and believes that it is all just a dream, he decides to join the military as a cadet with the help of Yuuko. Soon, he meets many more people that he knew, including alternate versions of all his friends, except for a single important person: his childhood friend, Kagami Sumika.
With time, he received military training and learned even more about this new world and the people of it, although he is troubled by the fact that he is dead weight compared to the rest of his team. During the Invasion of Niigata, while Yokohama Base was at DEFCON 2, the reality of the situation he was in finally started to sink in and Takeru experienced a panic attack and fainted. His Instructor deemed it a normal occurrence and attributed it to the fear and terror of the possibility of real combat. With some help, he manages to recover and gets back into the flow of things. Because of the war with the BETA, electronic games are virtually non-existant. As such, everyone spent all their childhood playing retro games such as bag-tossing, marbles, cat's craddle, kendama, shogi to the point where being an expert at such games was the norm.
After passing the Comprehensive Exam, his team is finally allowed to begin their Tactical Surface Fighter training. During their simulator training session, Takeru watches as each and everyone of his squad mates, who all were much more physically fit than him, get absolutely destroyed by the aptitude test. When it's finally his turn, he notices that all the shaking is hardly different from an amusement ride. He was so relaxed during the test that he almost fell asleep. Later however, he once again experiences a panic attack upon encountering a silhouette of a BETA and is unable to hear his Instructor's worried calls as his body enters fight or flight conditions and he starts screaming at the BETA, challenging it to kill him (in the manga Takeru faints).
In Alternative, Yuuko proposes the theory that the existence of Shirogane Takeru of the Extra timeline may have fused with a part of the existence of Shirogane Takeru of the Unlimited/Alternative timeline. This may have caused Extra Takeru to inherit the fear of being trapped and eaten by the BETA that Unlimited/Alternative Takeru developed during the time he was held captive. This is more likely to be the cause of why he experienced the panic attacks during his training rather than the fear of real combat: Extra Takeru, coming from a peaceful world where war is far removed from his daily life, does not fully understand the terrors of war, much less so the terrors of fighting against the BETA, even mocking Yuuko of the Unlimited timeline when she initially tells him that humanity was waging war against an alien species.
Upon completion of the tests, to everyone's surprise it is revealed that Takeru scored the highest initial score on the aptitude test in the history of Yokohoma base. He is far from happy however and is so upset that his Instructor later takes him aside to talk to him about his panic attacks. She speaks to him with a rare kindness and attempts to lift his spirits by telling him that the base only accepts the best of the best, and among all those people, he came out on top. Takeru then turns the tables and integrates his skills from Valgern-On into TSF piloting, confusing his Instructor and making his squad mates uncomfortable: the "dead weight" of the group had become "the best" at the one thing that mattered in the end.
It was thanks to Takeru's unconventional piloting and aptitude that Yuuko pulled some strings to bring the cadets' training TSFs faster, to further study the boy's skills. After the TSFs are delivered, the squad notices an extra unit, the Type-00 Takemikazuchi, brought in by Lt. Tsukuyomi Mana of the Royal Guard, for Meiya's personal use. Takeru is oblivious to its significance and his squad ignores his questions because they think he was making a terrible joke. Takeru is later confronted by Mana when he goes to have a closer look at the unit. She catches him off guard when she refers to him as "Shirogane Takeru", for that was the first time anyone in Unlimited recognized him. However, Mana interpreted his surprise as an admission of guilt, justifying and reinforcing her fear for Meiya's safety and she proceeded to interrogate him harshly. She surprised him even more when she asked him why a "dead man" was walking. This continued until Meiya intervened and sent them away. Thinking Takeru was feigning ignorance, Meiya reluctantly tells him that she's a "relative of the Emperor" but refuses to go into detail. Though Takeru was shocked at being told that he was supposed to be dead, he got over the surprise quickly and there was no further mention of it.
After he was imprisoned because of his actions during the civilian evacuation operation, he came back to a gloomy base. His squad was told to spend their time as they wish, much to his and his squad's surprise. Noticing that, besides them, everyone was in a rush to do something and Yuuko even pushed him away when he went to see her, he decided to throw a Christmas party to raise everyone's spirits. During the celebration, Marimo breaks down into tears for unknown reasons, making Takeru wonder out loud if she "got dumped again", to Marimo's anger. Takeru heads to Yuuko's office only to find her completely drunk, having consumed excessive amounts of high quality alcohol, and in a state previously inconceivable with her demeanor: bemoaning her fate and the fate of humanity, crying to Takeru about being unable to fit "15 billion semiconductors in the palm of a hand", screaming that she's a genius and everyone else is just stupid and even laughably ordering Takeru to tell her that she's a genius. Depending on certain factors (see Yuuko's page) Takeru will either stay or return to the party.
Everyone is recalled into the classroom by Marimo's voice over the intercom. There, Brigadier General Paul Radhabinod, the base CO, makes his first appearance. He tells the squad they were secretly part of a military experiment, Alternative IV, and that the plan had now officially progressed to its next phase, Alternative V. He thanks them for their efforts and tells them that their efforts weren't in vain before departing. Takeru impulsively stops the CO and asks him about Alternative, but the CO kindly tells him that he is nothing but a pawn, and if it weren't for Marimo's request he never would have told them any of this information.
The game then skips two years ahead in time, during which the details of Alternative V were revealed and the squad was promoted to 2nd Lt. with Takeru earning the position of a squad Leader. However, since some of his squad mates were still important political hostages (depending on which girl he courted), they were only piloting Type-77 Gekishin's instead of Type-94 Shiranui's and put on guard duties, far away from the front lines.
Before the last shuttle is launched, Takeru either convinces his pregnant girlfriend to leave Earth or loses heart and decides to stay with her and breaks his boarding pass. As they return to their squad, they find out Kasumi is missing. Takeru rushes to floor B20 and tries to persuade Kasumi to board the shuttle, but she evades him and then shocks him when she screams "You wouldn't understand Takeru-chan!". Takeru eventually persuades Kasumi to leave. He decides to fight for this new world, even giving his life if necessary. In a world that has lost hope, with humanity that has decided to leave Earth, he chooses to stay and fight to the bitter end.
If Takeru had convinced his girlfriend to leave, an after credits scene shows his girlfriend and his child staring at a star in the sky on a wide green field. The mother tells her daughter that the star in the sky is called Earth and she tells her about her father and how he is fighting for their sake. The little child, in her innocence, starts happily shouting "Good luck father!" multiple times, causing her mother to silently break down into tears.
The universe then diverges into an infinite amount of outcomes: two possible paths are shown in the Muv-Luv Alternative manga and Muv-Luv Unlimited The Day After. The one in the manga shows Takeru piloting a Type-77 Gekishin during a battle where his unit is overrun by the BETA. He is then overshadowed by a Fort-class and starts to fire his weapon, and continues firing even as his TSF is ripped apart by the BETA. It is implied he was killed after that exchange as he wakes up and enters into the eventual "Alternative" loop.

Time Loop

Once again Takeru wakes up in his room, this time believing that the events of Unlimited were just a dream. However, he quickly notices that something is wrong: he has been sent back in time to the beginning of the events of Unlimited. Instead of letting humanity abandon earth once more, he decides to do his utmost to prevent that outcome. The solution: helping to complete Alternative IV. He shares his knowledge of the events of the Unlimited timeline with the vice-commander of Yokohama Base, Professor Kouzuki Yuuko, and though initially met with suspicion, he convinces her to give him an opportunity to prove himself. He joins the military as a cadet once more; however, unlike last time, he is equipped with the knowledge and the physical fitness he gained during the years he spent in the Unlimited timeline. Excelling at everything, he rushes through training, pulling his comrades with him, always looking for a way to change the future positively.
Soon, the future does start changing, but not necessarily in the way he had hoped. After witnessing incredibly tragic events firsthand, he is diagnosed with PTSD and becomes depressed, to the point where he had almost given up hope. But after finally regaining confidence in both himself and his mission, he gets back on track with the help of Yuuko and his comrades. Learning many things about humans and how the world works in the way, maturing both as a person and as a soldier, Takeru gives everything to complete his objectives, losing many important things in the process, but also regaining others, always believing that the future he will obtain will be a precious one for Earth.
The fate of Shirogane Takeru of the Unlimited/Alternative timeline is revealed towards the end of the game. Both he and Sumika were captured by the BETA and held in a "concentration camp" somewhere in the Yokohoma Hive prior to the deployment of G-bombs. Part of a large group of humans, he struggled to keep his sanity as everyone around him was dragged away by the BETA for unknown reasons. Eventually, only he and Sumika remained. A soldier class BETA then attempted to drag Sumika away as well, but Unlimited/Alternative Takeru attempted to fight them off barehanded and was quickly ripped apart and eaten in front of his friend. Although he faced a pitiful death, his sacrifice caused a powerful shock to Unlimited/Alternative Sumika and was a major contributing factor in allowing the Shirogane Takeru of the Extra timeline to cross dimensions.
In Unlimited/Alternative, Extra Shirogane fuses with Unlimited/Alternative Shirogane to form a causality conductor. He is formed as a flawed combination of all past Shiroganes from the previous time loops, giving him experience and (flawed) knowledge of the future. The memory retention between loops isn't perfect, if Shirogane learned something critical on his second loop he will not remember it on his third or fourth loop, but he needs to experience the same event many, many times for him to remember it, Yuuko hints at this during her ending in Unlimited.
Interestingly, this effect carries on to his body as well, for Shirogane's accumulated muscle memory also carries on with into each loop, this is shown in Alternative where Shirogane is extremely fit for his age, and extremely experienced with a variety of weapons (especially TSFs). This means Shirogane also retains his sex skills during time loops, meaning that by the time of Alternative, Shirogane's skills during sex should be on the same level as his skills as a soldier given all the practice he's had with the court-able characters in Unlimited. Yuuko confirms this in her ending when she praises Shirogane's skills.
Logically, this process of accumulation of mass with each loop should have increased Shirogane's brain mass as well, leading to a very sharp increase in his intelligence, however, as Alternative shows, Shirogane remains nothing more than a slightly intelligent teenager. What this means is brain mass doesn't accumulate in the same way as muscle mass, Shirogane wasn't very bright to begin with or the author deliberately limited Shirogane's intelligence for plot advancement reasons.