Kokonoe was born to two of the Six Heroes, Jubei and Nine, almost immediately after the end of the Dark War in 2110. Although she should have been born in a peaceful time, this was not the case. Not long after her birth, Nine was thrown into the Boundary by one of the Six Heroes, Yuuki Terumi. Terumi soon set his sights on the infant Kokonoe and found her, but before she could be murdered, she was saved by the Kaka Clan.
Jubei became a single parent whose majority of family and friends had been killed by either the Black Beast or Terumi. Jubei became a wanted fugitive and left Kokonoe in the care of the Novus Orbis Librarium's Intelligence Department. The Department never let her out of its sight as she grew up. Jubei's absence throughout her childhood strained the two's relationship.
At some point, Kokonoe left the care of the NOL and involved herself with Sector Seven, having become a member of the Committee. She ensured that their headquarters would be built on top of the First District to seal access to her mother's workshop, which even Kokonoe herself had struggled to enter. At some point, Kokonoe also became the first SS-criminal wanted by the NOL, but she hacked into their database and erased all traces of herself from their system.
Ikaruga Civil War
Spiral Shift, Remix Heart, Collisions, Determination, The Rat, that which is inherited, Trust You
After successfully retrieving Nirvana, Kokonoe took in a squadron captain who had barely survived an encounter with Azrael. She performed multiple operations on him and found that he was a compatible match with demon cells. She injected him with them and used cybernetics to replace what the cells failed to regenerate. When the captain finally awoke, Kokonoe gave him the name "Iron Tager" that she had invented on the spot and wrote some code to help him move more smoothly, ignoring his surprise at her beastkin heritage. Kokonoe performed subsequent experiments on Tager under the pretext of searching for a way to return him to how he previously was.
Before long, she sent Tager to Ibukido with the objective of retrieving the Prime Field within one of its laboratories. Tager managed to retrieve Lambda-11, and immediately returned to Sector Seven after Kokonoe warned him that Lambda-11 would rot if left for too long. 
In 2196, upon learning that the Burning Red Grimoire was possibly within the 15th Hierarchical City of Torifune, Kokonoe sent Kajun Faycott as an undercover spy to the academy. She contacted her once to tell her that readings of the Azure Grimoire had surfaced within the facility.  Kajun herself later contacted Kokonoe to give her a reading of a sample from an alchemy-based creature. The two deduced that a former Sector Seven researcher was lurking within the facility.  Later, Kajun reported to Kokonoe that both the incomplete Burning Red and the researcher had escaped. Kokonoe revealed that she had been planning to use the Grimoire to fuel Tager and resigned herself to finding an alternative. 
Sometime later that year, Kokonoe began to prepare for a salvage operation to retrieve Hakumen, one of the Six Heroes, from the Boundary.  She also outfitted Tager with an Artificial Causality Phenomenon Weapon.
Kokonoe traveled with Litchi to the 11th Hierarchical City of Shinatsu's Hazuki estate. Once there, she announced her presence by launching a projectile at Mai Natsume and Houichirou Hazuki, managing to make the latter step backwards.  She offered Mai the choice to either join her, or to be protected by her father . Mai chose to join her.
Kokonoe led Mai, Kajun, Litchi, Bell, Taro Sasaga'e, and Shiori Kirihito to Shinatsu's cauldron to use it to travel to Sector Seven, as teleportation was not an option with such a large group. However, they were assaulted by a group of Fuzzy who took Bell and Mai to Meifang and prevented the rest of the group from following. Kokonoe teleported Tager directly to her in order to help them fight off the Fuzzy.
In reality, Kokonoe had intended for the two girls to be bait for Meifang. She had already planned out the whole situation and arranged for help from Kagura, who sent Jin Kisaragi to assist Mai in fighting Meifang and the vampires. Through an Ars Magus, Kokonoe was able to listen in on Meifang and learned of her plan to recreate Gigant: Take-Mikazuchi by smelting the No-Name Grimoire with Bell. After an incredulous outburst from Kokonoe, Meifang claimed that Kokonoe was actually curious about the smelting and said she would destroy Sector Seven with Gigant: Take-Mikazuchi first.
Eventually, the Fuzzy army crumbled into dust just as Kokonoe had predicted, allowing her to conclude that they were remnants of the Black Beast. With the assistance of Tager and Litchi, Kokonoe teleported Taro, Shiori, and Kajun into a Phantom Field created by Meifang so that they could aid Mai. 
Under Kokonoe's orders, Tager placed various nodes across the 15th Hierarchical City of Kagutsuchi to restrain Hakumen should he appear. Later, Kokonoe used Phenomenon Intervention against Hakumen to interfere with his fight with Ragna the Bloodedge. She watched as Hakumen was defeated and then secured him, transporting him back to Sector Seven. She asked Tager to retrieve all the nodes he had placed earlier since she did not wish to detonate them, and gave him the secondary objective of watching the events that were about to unfold near the Sheol Gate.
Through Tager, Kokonoe saw that Yuuki Terumi, the man who had killed her mother and corrupted Roy, had been revived. She taunted him, but noticed that the cauldron was set to detonate, so she cut herself short, relented, and ordered Tager to retreat.
A genius of a scientist working at Sector Seven and the "mother" of Tager, whom she created. She led the operation to salvage Hakumen, who had fallen into the Boundary, and although she stayed silent on Hakumen's actions afterwards, she did send Tager to monitor him from afar. Like so, she continues to experiment day and night, so that she may defeat "Yuuki Terumi."
A genius of a scientist working at Sector Seven and the "mother" of Tager, whom she created. She was born with the ears and tail of a cat. Although she sent Bullet and Tager to detain the "Grim Reaper" who had appeared in Kagutsuchi, she harbors doubt about the very world itself. Following the mystery of "Who exactly is the Hakumen of the Six Heroes that I salvaged?" she decides to head to Kagutsuchi herself.
Kokonoe gave an explanation of the events surrounding the last few months to Hibiki, Makoto, and Tager. Celica reported to her the details of Jin’s injuries – before long, Kokonoe noticed that Noel had been teleported out of the facility, but before she could act on it, she was absorbed into the Embryo.  Her memories were altered so that she never remembered salvaging Hakumen, reviving Celica, Lambda’s death, and also believed that Bullet had always been a member of Sector Seven. She too was forced to believe the date was 12/31/2199.
Inside the Embryo, Kokonoe began searching for the Azure Grimoire, and deployed both Tager and Bullet to find it. Mai had volunteered to go down to assist in their mission, and Kokonoe gave her some data pertaining to her objectives, but warned her to not go near the Azure Grimoire whatsoever due to her state. Mai went to make the scientist coffee, reminding the latter of when she had Roy under her wing.  When Tager found Ragna, she asked him some questions, buying time for Kagura and an NOL squadron to arrive to apprehend him. 
Personally, Kokonoe made her way to Kagutsuchi, and stayed inside the NOL branch where Hibiki issued her a fake ID. She came because of the appearances of Celica, Hakumen, and Naoto Kurogane – the former two, to her distorted memory, should not be in the time-period, and the latter does not show up on any database. 
A massive phenomenon event occurred, forcing Kokonoe into Ikaruga where she heard the voice of her mother, Nine, calling her to kill Izanami and claim her piece of the Azure, Initially shook by hearing her voice, a voice she had not heard for over 85 years, she contacted Tager and began a rendezvous plan, making her way to Yabiko.  She received another call from Tager later on when he encountered Arakune; she initially ordered that he capture the monster, but after seeing that he had a compressed core of seithr in him, similar to a Nox, she ordered that he retreat as they had no new data on him. 
Tager found Hakumen wandering around Ikaruga. She asked him to come back to her laboratory so she could gather data, but he refused, telling her to find her own path  Now in Yabiko, Kokonoe, Kagura, Hibiki, and Tager all discussed the differences in their memories. Again, she looked back on how Hakumen and Celica could still be in the timeline and how too many coincidences were lining up with one another.  Kagura came back with both Mai and Noel in tow, and the conversation continued.  Kokonoe later spent her time fixing the differences in data using her memories, now fully returned to her. 
In time, Celica returned to the Yabiko branch where Kokonoe was staying. She explained to her aunt that she was unable to find her due to her teleporter’s coordinates being distorted by the Embryo’s landscape. , She found Celica’s memories unaffected by the Embryo and deployed Tager to tackle Ragna, knowing that he could be starting something serious.  Rachel later asked her to help with locating Ragna and she complied, finding him near Ibukido and bringing him back to Yabiko.  She performed maintenance on his arm and the Idea Engine. She warned him about the power he was using, and about Celica’s existence having the probability of disappearing at any moment. She explained to everyone about the hidden eleventh Nox Nyctores, the Corpus Sepulcro: Requiem and how she built Sector Seven’s headquarters over her mother’s workshop. It would not be long until both Jin and Jubei arrived to tell her that it would be impossible to break into the workshop through brute strength alone. Kokonoe realised this, knowing she could not use her blood to enter the workshop due to her beastkin heritage. 
The following morning, Kokonoe was part of the strike squad sent to Nine’s workshop. Inside the workshop, Nine defeated Jubei and told the group her desire, about the world, the Prime Field War, and why she created Requiem. She watched as her mother was defeated by Ragna and sent on her deathbed, understanding why as she opposed her mother’s ideals to create a new world.  Kokonoe defended Nine when Izanami arrived to kill them all, but had no choice but to watch her use the Radiance of Extinguishment and teleported out of the area after she watched her mother die – she was forced to leave her father behind in the area as well. 
Kokonoe arrived at her aunt’s church, completely intact. She marvelled at it for half-an-hour before the others arrived, presumably because of the desynched time caused by Requiem. She soon left for Yabiko, handing Rachel a communicator in case anything should happen to Celica and Noel. Back at her lab, Kokonoe realised the only way to access the frozen space-time to save Jubei and destroy Requiem would be to take measurements from Naoto Kurogane . She teleported to his location in Ikaruga and battled him to take data measurements, but scared him off when she was unable to have him return to the laboratory. She teleported back and deployed Makoto to capture him. She did have enough measurements to form a hypothesis. 
With her hypothesis, Kokonoe gave her master plan to kill Izanami, destroy Requiem and save Jubei to a group consisting of Kagura, Lambda, Minerva, Ragna, Noel, Jin, Trinity, Hakumen, Tsubaki, Tager, and Rachel. An Embryo floated above Ikaruga, and they would enter it to venture to end up above the frozen space-time where Requiem existed. Tsubaki would create a Zanki Barrier to ignore phenomenon intervention, and Hakumen would cut through time to save Jubei. Furthermore, Kagura would deal with Azrael, Ragna and Rachel with Terumi, Lambda and Tager with coordinates, Minerva with Requiem’s destruction, and Noel with Izanami.  Her plan fell apart, however, when Izanami managed to scatter the group across the space-time and took Requiem, transporting it elsewhere. 
Makoto succeeded in her mission, and Kokonoe deployed both her and Naoto into the frozen space-time to back up the others. She heard of Kagura and Jin’s success in defeating Azrael. She was visited by Es, who backed up her data and told her that the Doomsday was still commencing. Kokonoe contacted Ragna and Noel afterwards, knowing that Requiem was now destroyed and Izanami absorbed, warning Noel to be careful with what she remembers, and ordering them to find the Amaterasu Unit and send it back into the Boundary so a new possibility can be born. 
Almost immediately after Es left, Kokonoe began evaporating into seithr. She created a backup of herself using accumulated data and Sector Seven’s remaining energy. The backup guided the remainder of the group after Susano'o was reborn, and passed on all the data it could to Trinity. She told Jubei to apologize for his parenting to the real Kokonoe, and not the backup, in the next world. 
In the new world created by Ragna, Kokonoe gave assistance to Tager and Bullet on a mission in Yabiko. She kept watch over the Dog House where Azrael slept. 
- BlazBlue: Chrono Phantasma, Arcade Mode, Kokonoe - Mad Scientist
- BlazBlue: Chrono Phantasma, Story Mode, Six Heroes, Episode 01
- BlazBlue: Central Fiction, Story Mode, Episode 001, Chapter 001
- BlazBlue Material Collection, Iron Tager Short Story - Trust You
- BlazBlue: Remix Heart, Chapter 10
- BlazBlue: Remix Heart, Chapter 19
- BlazBlue: Remix Heart, Chapter 25
- BlazBlue: Calamity Trigger - Part 2, Chapter 1 - Orient Town
- BlazBlue: Variable Heart, Chapter 13
- BlazBlue: Variable Heart, Chapter 14
- BlazBlue: Variable Heart, Chapter 15
- BlazBlue: Variable Heart, Chapter 16
- BlazBlue: Variable Heart, Chapter 18
- BlazBlue: Calamity Trigger - Part 2, Chapter 5 - Calamity Trigger, Successor to the Azure
- BlazBlue: Chrono Phantasma Official Site (JP), Kokonoe
- BlazBlue: Central Fiction Consumer Edition Official Site (JP), Story - Kokonoe
- BlazBlue: Central Fiction, Story Mode, Episode 001, Chapter 002 – 006
- BlazBlue: Central Fiction, Story Mode, Episode 003, Chapter 015, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 003, Chapter 021
- BlazBlue: Central Fiction, Story Mode, Episode 004, Chapter 023
- BlazBlue: Central Fiction, Story Mode, Episode 005, Chapter 036, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 005, Chapter 038, Sub Scenario 2
- BlazBlue: Central Fiction, Story Mode, Episode 006, Chapter 042, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 006, Chapter 049
- BlazBlue: Central Fiction, Story Mode, Episode 007, Chapter 055
- BlazBlue: Central Fiction, Story Mode, Episode 008, Chapter 063, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 009, Chapter 067
- BlazBlue: Central Fiction, Story Mode, Episode 009, Chapter 069
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 07
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 079
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 081
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 082
- BlazBlue: Central Fiction, Story Mode, Episode 010, Chapter 084, Sub Scenario 1
- BlazBlue: Central Fiction, Story mode, Chapter 084, Sub Scenario 1
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapter 088 – 089
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapter 090
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapters 090 – 091
- BlazBlue: Central Fiction, Story Mode, Episode 011, Chapter 092
- BlazBlue: Central Fiction, Story Mode, Episode 012, Chapter 100