Back at school, Suguru now has to explain his new lifestyle to his friends, since it's pretty difficult to hide the fantastic lunches that Mahoro packs for him and the well-pressed clothing that he now wears. His close friends, Hamaji and Kawahara are immediately infatuated with Mahoro's beauty, while Miyuki and Rin are slightly jealous of the same. And then there's Chizuko, the Food Connoisseur, who is completely taken with Mahoro's cooking expertise. To round off this cast of characters, Ms. Shikijo, their over-sexed school teacher, has an instant dislike for Mahoro and the attention she commands from young Suguru. This causes Ms. Shikijo to set her goal in seducing Suguru away from Mahoro. This, in addition to Mahoro's dislike for lewd and indecent behavior, has automatically created a competitive atmosphere between the two ladies. So watch out when the battle begins!

After Suguru's water heater breaks, Ms. Shikijo and Mahoro's rivalry explodes during a visit to a Bath House where Miyuki's family works. July 19th, and school has ended. July 20th marks the day that Suguru's father has passed away. In memory of his passing, Suguru asks Mahoro to accompany him to the gravesite, not knowing that Mr. Misato had once worked for Vesper and served as Mahoro's superior in this secret organization. Not only does Suguru feel the loss of his father, but Mahoro, equally, if not more so is torn at the loss of Suguru's father for reasons that only she knows.

It's summertime and a everyone travels to the beach for some fun in the sun! However, things go awry when an alien anti-android robot appears and strips off all the female bathing suits *ahem*. Mahoro must now return briefly to her combat mode to take care of this threat. Will she be able to take care of this now that she has discarded her combat armor?

During a VESPER staff review of Mahoro's life and activities following her entry into civilian life, a letter from Mahoro is read to the assembled officers. In it, she describes taking part in a "summer vacation group research trip" to explore the notorious "nine mysteries" of Hiryu School 4. Seven of these are generally acknowledged to be no more than standard rumors typical of any school; the remaining two, however, have not been as easy to put to rest. Of course what Suguru, Kiyomi and Toshiya don't know is that all through, the three girls, minus Mahoro, are playing them, as part and parcel of their own "human response to stress" research project. But seek, and ye shall find: it does not take much to send them running frantically through the school to get away from "red-haired Ando", according to legend, a girl who fell to her death from the school roof years ago and has been haunting the halls at night ever since. Mahoro herself is in on the joke, though she plays along. The twist, however, comes when, after becoming separated from the group, she comes across the real Ando, a ghost or spirit trapped in the school until she can confess her love to a boy whose own spirit is trapped in another part of the building. Reunited by Mahoro, the two ghosts, now freed - and together - disappear, and the letter concludes.

As the number of contacts between SAINT and humans increases, VESPER officers agree that alone and stripped of most of her combat capabilities, Mahoro is in danger. To counteract this threat, her combat support mech unit, V1046-R9 Slash Zero, is authorized to join her in the human world. In the meanwhile, the Hiryu town Summer Festival is fast approaching. Each year, the leading citizens of the town select one girl to be featured in the hours-long Dance of the Dead, a grueling performance that pushes one to the limits of her abilities and endurance. This year, Mahoro is the one chosen. In the few days remaining before the Festival, then, she is occupied almost entirely with pracicing the dance. The question of what to wear for the event, which calls for traditional clothing, is answered when Suguru pulls his his mother's yukata and Cmdr. Misato's kimono out of storage. After extensive practice, Mahoro performs magnificently, dancing nonstop for three hours and eleven minutes. According to one of the residents, hers is the best dance in at least a decade. Following the conclusion of it, her and Saori, herself chosen to perform several years earlier, engage in some not-so-friendly "competition" at the various festival booths, with Suguru as the prize - which leads, in short order, to both of them being banned. As the festival comes to a close with a fireworks display, Suguru remarks that this is the first time since the death of his parents that he has been able to actually enjoy himself. In due time, as him and Mahoro rejoin the rest of Suguru's classmates to watch the fireworks, he asks Mahoro to come to the festival next year, as well. Knowing what he still does not, though, she pauses. Her answer, "it'd be nice to come again," - nothing more, and nothing less.

The summer vacation comes to an end, and Suguru, Miyuki, Rin and the others return to school. On the very first day, as they are walking to class, Chizuko is nearly run down by an out-of-control car, but saved by a mysterious man who appears, seemingly out of nowhere, and leaves as quicky. Later in the day, the same man, Tou Ryuga, reappears again, as a substitute teacher hired by the school. But later still, at the mention of his name, Mahoro grows uneasy. The reason, revealed in the evening of the same day, is simple: much like Mahoro herself, Ryuga is a combat android, only in the service of the alien invaders SAINT. He attacks Mahoro as she is out shopping, and although Mahoro and Slash gain the upper hand, she feels that rather than being able to defeat Ryuga, she is merely being allowed to survive. Before he leaves, however, Ryuga declares his intention - to challenge Mahoro and make the final determination of which one of them is the better warrior. During Mahoro's active service, her and Ryuga engaged - inconclusively - several times. Now, though, the first step he takes is finding out just what the nature of the relationship between Mahoro and Suguru, whom he knows to the the son of Commander Ryoh Misato, is. It is to this effect that he infiltrates Suguru's school and interrogates his various friends. The responses are nothing but praise - and in the cases of Miyuki and Rin, blushing and mumbling - although unsurprisingly, Saori misinterprets the situation and perceives Ryoh as a rival for Suguru's affections. Later, Slash and Mahoro, who also infiltrate the school, challenge him. Mahoro threatens to fight Ryuga right there and then, if that would mean protecting Suguru. Whether he is truly concerned or simply looking for an excuse to put the battle off is not clear, but he declares that he is unwilling to fight in a location where civilians could be harmed, and leaves.

As SAINT combat android Tou Ryuga enters the lives of Suguru and his friends, disguised as a substitute teacher, Suguru becomes aware that some sort of connection exists between Ryuga and Mahoro. To further understand their relationship, Suguru invites all of his friends, as well as both Ryuga and Saori to a party at his house. At the same time, Mahoro is becoming more and more aware that her view of herself - as well as her relationship to Suguru - is changing the more she time she spends living with him. Originally, she saw herself as merely atoning for causing Commander Misato's death, but as the days go by, she comes to realize that what she is truly looking for is a place to belong, a home to be able to take care of and come back to, and people to care for. In contrast, Ryuga's self-examination shows that he sees his entire raison d'etre as fighting - and defeating - Mahoro. His entire identity is of a warrior who was defeated once but is desperate for a second chance, because without it, he is nothing. The party at Suguru's house, where Ryuga comes to realize that Suguru, despite suspecting the depth of Mahoro's past is still unaware of his role in it, sets the stage for the final confrontation between the two combat androids. However, Suguru's intervention means that the actual duel will take place two days later, in a mutually agreed-upon location. With the time and place of the duel now determined, Mahoro again faces the fact that Suguru still has no knowledge of her impending death. She has already caused him immeasurable pain once, and is left to wonder - it is worth living just a few more months with him if the end will still be same pain.

With the time and place of the final duel with Tou Ryuga now set, Mahoro really has nothing left to lose, and uses the opportunity to ask Suguru out on a "date" to Yokohama. The effect is predictable: both him and Saori are prompted to imagine all the romantic implications of such a situation, and of course, when Mahoro and Suguru finally depart, Saori is right there, pursuing them on her Vespa. It's an uneven match, but the woman certainly gets points for persistence... The "date" itself is absolutely idyllic, as per Mahoro's expectation of "fun, tea, fun, lunch...and then more fun!" - an amusement park trip, shopping, lunch, then the warm early fall evening at a park. And when she reveals Ryuga's true identity to Suguru, he is not particularly surprised. Later on still, as Sugur and Mahoro are gazing over the nighttime city, she tells him that since beginning to work at the house, she has been able to find happiness. But when in Suguru's reply, it is clear that he knows there is much more about her - and about her relationship to him - that she is not telling, Mahoro can't help but face the full weight of reality: her past, her loneliness, and the fact that she is very much living on borrowed time. Suguru then plays his hand and asks Mahoro to explain her past as a combat android when she feels she is able to do so. After they return home, Suguru, tired, goes off to bed, though despite being exhausted, he is unable to fall asleep and lies there, thinking. As soon as he heads out, though, Mahoro changes into her battle outfit and sets out for the duel with Ryuga, determined, however, to defeat him - and to come back alive...

A flashback episode, "Fate as a Warrior" shows Mahoro as a Vesper combat android, undergoing training and fighting her first battles. Endurance tests under various extreme environmental conditions, while too short to be truly useful, nonetheless succeed in giving her an appreciation of life, and her first battle is an overwhelming victory. The episode also shows fully the battle in which Cmdr. Misato, really the first person to accept Mahoro as more than merely a weapon, lost his life. It is the memory of his life - and his death - that really leads Mahoro to accept the full weight of her own existence, and to desperately want to continue living for as long as she can.