We first learn of the state of the world thanks to a narration by Tatsuya. Also we meet the main characters Tatsuya and Kiyoko who are on the run from debt collectors. We also are introduced to Sex, Octo and Novem. The first three of the Gilgamesh we meet. We also see the heaven's gate facility for the first time.

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Three sinister figures visit the house, which was thought to be safe. The others decide to deal with the situation and ask the siblings to stay inside. However, the two want to know what is happening outside and encounter a monstrous creature. Regaining consciousness, Kiyoko and Tatsuya find themselves in a car with the three individuals who had been outside the house; they intend to take the siblings to the Countess. Kiyoko and Tatsuya do not fully understand what is going on, but they suspect it has something to do with their late father.

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The countess asks the children to stay only for dinner, assuring them they are free to leave afterward. During the meal, they learn that the three figures from the abandoned house are known as the "Gilgamesh." The countess wants Kiyoko and Tatsuya to help her fight them; however, neither wants to be exploited by her or the Gilgamesh, so they attempt to flee when the latter break into the countess's mansion. Ultimately, the situation resolves with the debt collectors reappearing at the door and the wealthy lady taking over the siblings' debts—on the condition that they help her.

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Kiyoko and Tatsuya resign themselves to their fate only reluctantly. The Countess takes them to the Hotel Providence, which is to become their new home. Upon arrival, they admire their spacious room and the beautiful garden visible from the balcony. Yet, the situation remains highly mysterious and unfamiliar. It does not take long for an incident to occur: the severed wing of one of the Gilgamesh attempts to break free and act on its own, but Tatsuya manages to stop the strange body part.

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A new piano is delivered to the hotel, as the old one was destroyed during the fight with Una's Schwinge. Afterward, Kiyoko attempts to teach Fuko how to play the piano. Tatsuya learns that the others possess a special power known as "Dynamis" and that this power can be passed from one person to another; however, Kiyoko does not appear to be receptive to it. In the middle of the night, an alarm suddenly sounds, and everyone rushes to the hotel lobby. The Countess orders the siblings to return to their room, but upon entering, they find the setting transformed to look exactly like the abandoned house from the past. The situation with the fireplace is also identical to how it was before. The Gilgamesh then succeed in capturing Kiyoko.

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Kyoko is still being held captive by the Gilgamesh, and Tatsuya and the Countess's servants set out to rescue her. Their path leads them to an abandoned airfield, where they find Kyoko near the wreckage of an old plane. However, the group is being watched; Kyoko and her brother Tatsuya are told to flee while Isamu and the others deal with the Gilgamesh. The siblings run until the Countess pulls up in her car and picks them up. Meanwhile, Novem is wounded in the ensuing battle, and Isamu attempts to take him along, but without success.

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It has snowed at the Countess's estate, and Isamu and the others head outside for a friendly snowball fight. However, Tatsuya is expected to train and utilize his abilities during the activity, revealing just how much progress he has made. Meanwhile, the Countess checks on Kyoko to see how she is faring after all the examinations and tests. Kyoko, however, is far from pleased by the visit and would much rather leave the place. She discusses this with Tatsuya later that evening, though he struggles to understand her perspective, as he actually finds the Countess's estate quite pleasant.

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Kyoko has disappeared, though Tatsuya isn't really surprised given the conversation they had the day before. Isamu sets out to look for her, but in the meantime, some of the Countess's people bring her back to the hotel, where she is initially locked up. Later, the Countess needs to settle a few matters with her, and it is agreed that Kyoko may leave. From now on, she is on her own and must pay off her mother's debts herself. Tatsuya is far from happy about this and is saddened that his sister will no longer be with him.

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Isamu and the others show Tatsuya around the corporate city. However, Tatsuya isn't particularly impressed and takes it all in stride. The Countess arranges a meeting with an old acquaintance who works for a major corporation and aims to restore the original sky, finally putting an end to the reflection. Suddenly, the Gilgamesh appear and a battle breaks out, though Tatsuya is unsure exactly how to handle the situation.

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A chase ensues, quickly escalating into a fight. Both Fu and Tatsuya struggle against their opponents at times, but fortunately, they survive the encounter with the Gilgamesh virtually unscathed. After this exhausting ordeal, they decide to make the most of their remaining time by having some fun. Fu browses through a few clothing stores and later talks Tatsuya into winning her a stuffed animal from a claw machine. While doing so, they run into three pushy guys who try to hit on Fu, prompting Isamu to intervene. He ends up taking a beating for it, however, as they are not permitted to use Dynamis in public.

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The urge to ask more questions continues to grow within the young people, and to pursue this, the four decide to head to Midnight Corp. There, they find a wealth of books in a library; with Dynamis's help, they attempt to absorb as much knowledge as possible to share among themselves later. Unfortunately, their reading session is interrupted by a rush of cyborgs that they are forced to eliminate. During the fight, they notice that these are not mere robots; beneath the metal plating lies organic material—and what puzzles the group even more is the inscription "ORGA" found on the creatures.

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The day has finally arrived for Tatsuya to meet up with his sister again. They have arranged to meet at an amusement park, and both are delighted to see each other upon arrival. After a pleasant afternoon, they bid each other farewell, and Tatsuya returns to the Countess's estate. Meanwhile, the Countess is on her way to visit his sister as well, seeking information about Tatsuya's mysterious birth.

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The Countess has been invited to a pre-funeral ceremony, and her presence is urgently requested. The person in question is the President of Midnight Corp. himself—someone who has known the Countess (or "little Hiroko," as he used to call her) since birth. During the festivities, Tatsuya suddenly suffers a fainting spell and has to be taken indoors to recover. After a while, however, he feels better, and it is decided that they should have something to eat. At that moment, the Gilgamesh launch an attack but are successfully driven back.

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Tatsuya and the others are practicing in the courtyard, and he is doing quite well. He has noticed Fu sneezing repeatedly and suggests she get it checked out. Isamu then explains that this happens whenever someone she really likes is nearby—and that the person in question is Tatsuya. Surprised by this news, he is unsure how to act around her. Meanwhile, the Turangalila Tower is brought online.

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The activation of Turangalila is a resounding success and is being celebrated in grand style. Tatsuya and the others are present as well, though the relationship between him and Fu is somewhat strained following yesterday's incident; consequently, he goes looking for her. Shortly thereafter, the Gilgamesh infiltrate the tower; they actually succeed in sabotaging it and sealing off the small view of the blue sky once more. However, the Blattaria—a special unit—then appear on the scene, attempting to stop the Gilgamesh by forcing them to materialize, thereby killing them.

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The October Project has thus more or less failed, and many people have been seriously injured amidst the chaos caused by the Gilgamesh. Isamu and the others are therefore trying to help wherever they can. Meanwhile, the Blattaria have tracked down Una and are hunting her, eventually managing to catch and kill her. At the same time, Kiyoko encounters Novem—one of the Gilgamesh—who collapses in front of her. She takes him to her home, where he subsequently regains consciousness.

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The Countess's hotel is quickly converted into an emergency shelter for the many injured people; everyone there is doing their best to help. Meanwhile, Novem remains with Kiyoko. Kiyoko considers her father's plan to create a new humanity—destined to live in a better world—to be utterly ridiculous. Shortly thereafter, an evil presence approaches the Countess's estate. However, it soon becomes clear that this is not the Gilgamesh, but the Blattaria. They break into the house, intending to take Tatsuya into custody; investigations—which the Countess dismisses as fabricated—have implicated him as the one responsible for the Gilgamesh's successful incursion into Turangalila.

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Tatsuya remains in the custody of the Midnight Corporation, where he learns that he is a clone of his father. Shortly after this shocking revelation, he is released thanks to the Countess, but the new knowledge weighs heavily on his mind. He runs away and heads toward his sister's place. Upon arriving, he encounters two of the Gilgamesh inside her apartment. Before Kiyoko can say a word, the Blattaria attack the building, forcing them to flee. After the battle, the Countess offers to let Kiyoko live with her again.

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Back at the hotel, it is time for bed. After a nightmare, Tatsuya wakes up and looks toward his sister, only to find her missing from her bed. He discovers her huddled beneath the piano in the lobby. Tatsuya sits down next to Kiyoko, and both fall asleep. Meanwhile, the other three pay a visit to the head of the Midnight Corporation to seek answers to their questions. There, they learn that—like Tatsuya—they are clones created by scientists. Shortly thereafter, the Blattaria attack the hotel but are quickly defeated.

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Fu and Tatsuya play the piano together and grow a little closer. Shortly thereafter, Kiyoko returns to the hotel. However, her stay is short-lived; after a brief conversation with the Countess, she collapses and has to be taken back to the hospital. There, childhood memories resurface; when she eventually regains consciousness, the first person she sees is Tatsuya. He had been by her side the entire time, but she soon begins to feel quite cold, so he leaves the room after a while to inform the Countess.

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In Uruk, Tatsuya and Kyoko's father encounters their mother. Together, they discover the tomb of Gilgamesh—the supposed source of Dynamis. Scientists from around the world join the effort to study the discovery in greater detail, leading to the establishment of Heaven's Gate. During this period, Kyoko and Tatsuya's mother is pregnant and is set to be returned to Japan to ensure the unborn child is not harmed by Dynamis. In the present day, the other Orga children learn the truth about their pasts—specifically, the circumstances of their birth. Fu struggles to come to terms with this revelation.

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The Countess tells Isamu more about the past and how she first met Enkidu. At that time, research at Heaven's Gate was in full swing, and the Countess was working there as a scientist. However, one day a mysterious life form was discovered; shortly thereafter, all experiments were halted, and Heaven's Gate was completely shut down within a year. This dealt a heavy blow to all the staff, especially since the very event Enkidu had predicted was coming to pass. All of this was overshadowed by a terrible accident known as "Twin X." During the incident, the Countess fell into a coma for several years, and from that point on, she made it her mission to ensure the truth behind the event was uncovered.

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Kasamatsuri’s father has died, and he blames his adoptive sister, Reiko. Shortly thereafter, she leaves her father’s estate and turns up at the Countess’s mansion. Meanwhile, new secrets regarding the Blataria are revealed: they are actually transgenic clones developed prior to the Heaven’s Gate incident. In the interim, Kasamatsuri has his father’s estate burned down and cleverly plants evidence to cast suspicion on Reiko.

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The Gilgamesh regroup and are once again at full strength. Having also acquired true Dynamis, they march into the final battle shortly thereafter. The true nature of the Blattaria is now revealed; they sweep through the streets, heedless of the cost, destroying everything in their path. Meanwhile, all the staff leave the Countess's mansion for safety reasons. Tatsuya learns from Kyoko that her father intends to unleash a so-called "Cleansing Flood" upon humanity to bring about a fresh start for the Earth.

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Toru is told that Reiko is not a girl after all, but a boy—something everyone apparently knew all along except him. At first, however, he is reluctant to accept this fact. During dinner, the idea comes up to take photos of everyone, since none exist yet. The photo session is interrupted, however, as the Blattaria attempt to stop the Gilgamesh from breaking into the Countess's mansion; for this purpose, they deploy a new machine created with Tatsuya's involuntary assistance. Shortly thereafter, Dr. Madoka appears in person.

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Final Showdown of the Gilgamesh.

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