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Oni is organized in 14 "chapters" (15 if you count the training course), also referred to as "levels" or "missions" :



The following was recently contributed to Wikipedia by an unidentified fan. As far as I can tell, it's been translated from a non-English version, as quite a few elements (e.g. quotes) are inaccurate. Please help improve this summary HERE.
It starts with an assault on laboratories by a criminal organization named simply as The Syndicate; who is being led by a mysterious, yet dangerous man named Muro. Konoko, through her neural link with the TCTF's AI Shinatama (actually known as an SLD, or Simulated Life Doll: an android programmed with Konoko's brain patterns), her connection with Commander Griffin and Dr. Kerr, moves in to investigate. All the while, Commander Griffin and Doctor Kerr are seen arguing over Konoko's situation, cut in from time to time by Shinatama reporting on her bodily functions (adrenaline spikes, likewise).
Konoko ventures into the warehouse and the mole of TCTF, Chung, is found dead at the scene. Konoko clears out the warehouse, and then is sent to the Manufacturing Lab belonging to the company that used the warehouse previously. Konoko has to stop a deadly AI brain (not surprisingly, also called "Deadly Brain") which can potentially destroy the entire city if reaching full potential, or even dominate the entire digital world. Upon her exit, she is called to a Bioresearch Facility, which is under the attack of The Syndicate. Upon her arrival, Konoko faces Barabas; a hybrid creature (part human, part machine; possibly a Chrysalis Symbiote) that is one of the main figures of The Syndicate. Upon Barabas' retreat, Barabas messages to Muro, telling him that "She (Konoko) is too strong.".
Muro moves towards the nearest Airport to get himself out of there, with Konoko in hot pursuit. She loses Muro, but manages to land a tracking device on the plane. Muro, while departing, speaks to his henchmen, who inform him that "They do not know of the condition of the Chrysalis". Meanwhile, the TCTF loses the tracking signal from Muro´s plane, allowing him to escape.
Konoko then returns to her regular life. Shortly after, TCTF Headquarters itself becomes compromised by an excessive attack of The Syndicate. Entering there, Konoko finds out that Barabas has kidnapped Shinatama. Unable to control herself, Konoko first defeats Barabas, and then experiences a strange feeling overtaking her: what the game refers to as a "Daodan Spike".
Konoko tracks down Shinatama, and despite Griffin's objections, rushes to save her. All the while, Muro is torturing Shinatama to retrieve information in a nearby Atmospheric Conversion Center (a central facility to the recent civilization which filters poisons from the air). While venturing deeper into the facility, Konoko finally finds Shinatama. Shinatama says that she won't live, and in a heart-wrenching scene, reveals that Konoko's real name is Mai Hasegawa, and that she was involved in some sort of project. Griffin, in a desperate attempt to prevent Konoko from getting further with that information, sets the auto-destruct sequence of Shinatama, revealing that the tiny robot was armed with a bomb with enough explosive power to be classified as a small nuclear warhead. Konoko flees, and TCTF starts pursuit.
Looking for her origins, Konoko goes to the Regional State Building, and there, is encountered by both TCTF and The Syndicate. She finds a terminal to access to the information, but as she is doing it, Muro's elite ninja, Mukade (possibly another Chrysalis Symbiote) swipes away the data concerning her. Konoko follows Mukade through the city's rooftops and finally, corners him. Mukade states that they are one and the same; that they should surrender to their essence, and revel in it. Enraged, Konoko kills Mukade and retrieves the disk.
Konoko goes back to Dr. Hasegawa's laboratory, wherein she discovers most of her past. Apparently, Dr. Hasegawa was a teacher, and had fallen in love with a student of his, Jamie, who was also an activist who believed that the government was hiding secrets. One day, Jamie and Dr. Hasegawa venture into a forbidden zone of wild life (overgrown plants were covering it), and Jaimie cuts her leg. However, in a matter of moments ("almost immediately", Dr. Hasegawa suggests) the wound gets infected and starts to kill her. Unable to bear seeing her in pain, Dr. Hasegawa shoots Jamie (to "ease her pain"). He has made a discovery through that incident, that the world outside of the atmospheric converters was extremely poisonous and destructive towards human biology. He leaves one note, "I will not let this tragedy happen again. Her brother will help me. He misses her as much as I do." Konoko learns that Jamie's maiden name was Kerr, and that she was Doctor Kerr's sister.
Konoko walks into the TCTF Science Prison to find Dr. Kerr, who tells her about the solution they developed. They had named it a "Daodan Chrysalis" which was basically a hyper-evolved form of a cancer cell. By implanting a person with the chrysalis, they would let it adapt to the biology which contained it, and grow as the host suffered damage, or experienced negative emotions (Which are met with hormonal spikes). However, further than that, over a duration of time, the chrysalis would start to grow the host as well, replacing the organs of the host with its own extensions. As Konoko asks about her past, Dr. Kerr tells that The Syndicate had discovered it, and Konoko's father was killed. Dr. Kerr also reveals that Muro is Konoko's brother, the child he left behind as he escaped with Konoko to TCTF in order to use the technology of TCTF and establish their security. Griffin, however, opposed greatly to the self-sustaining nature of the chrysalis and wanted it kept under strict control. Before he can reveal more, Dr. Kerr is killed by a TCTF Black Ops member, who attempted to shoot Konoko. After killing Kerr's killer, Konoko then decides to claim revenge on TCTF. To escape the Science Prison, she is forced to test the theory she has just heard, by attempting to escape through acid vats.
Konoko doesn't stop; she infiltrates the TCTF HQ single-handedly, all to learn that Griffin had used Shinatama to do something. Upon tracking Griffin down, Konoko finds out that Griffin constructed his own security cell with the defenses involving Shinatama, one that knows Konoko the best. As Konoko shuts Shinatama down, Shinatama begs Konoko to stop her, to kill her. In the end, as Shinatama's leftover body marches to Griffin, and Griffin shoots it down, Konoko takes the gun and holds Griffin at gunpoint.
(At this point, the player is faced with the choice of shooting Griffin or walking away. The choice has no effect on the overall plot. If the player chooses to shoot Griffin, the final showdown ensues between Konoko and Muro's new self as he has accomplished to pass to the next stage of Chrysalis evolution - the Imago stage. This choice makes the game somewhat more difficult to complete, as instead of fighting a large number of weaker enemies, one must face a superboss -- periods of invunerability, massive size and damage, etc. If the player chooses to walk away, then Muro stays in human form, he and his henchmen face Konoko, upon which Griffin comes along to help her. The overall plot remains the same, the ending included.)
Konoko reaches the mountain compound that The Syndicate is using. Upon her arrival, she discovers that Muro is planning to reroute the atmospheric conversion centers to pollute the clean world; a disaster from which only the Chrysalis can save humankind. As Konoko quotes, "He's planning to kill everyone who doesn't sell his soul to him for a Chrysalis." Quickly devising a counter-measure, Konoko tries to reroute the atmospheric conversion centers, but doesn't interfere in time. Instead, she has a single choice left: destroy the mountain compound and the conversion centers connected to it. Then, she heads to the rooftop to face Muro.
After the explosion, Konoko is shown roaming the ruins of the city, and monologuing to herself that, the Chrysalis may save humankind in the form of evolution after the disaster that had occurred, but that the fate of humankind is unclear.