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 13th 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."
At an unknown point in time, Kokonoe realized that to beat Izanami, she would need the power of her deceased aunt, Celica A. Mercury. To this end, she somehow interfered with the past. Celica, when she lived during the Dark War, was plagued with unusual dreams because of this intervention. These dreams included seeing a mirror of herself in a pure white room. A month after the war ended, Celica was drawn by Nirvana to the bottom floor of the cathedral in the Magister's City of Ishana. She saw another mirror which created a copy of her. The real Celica had no recollection of this event as became hazy, almost like a dream. The copy of Celica from the Dark War time period was taken by Kokonoe and put into her own time period of 2200. This copy was a Chrono Phantasma (Those Who Should Not Exist).
During a party that Kagura had, Kokonoe took the liberty of taking over his basement, converting it to her new lab. She took his bedroom and made it into an elevator, also getting a hold of new clothes for Noel and Makoto, anticipating their arrival and knowing that they would new outfits to avoid backlash from Ikarugans about being in NOL uniform. She took Tager away for maintenance after allowing Makoto and Noel free roam, telling her subordinate that she intended to fully oppose the NOL and that Azrael had been released.
Kagura later told Kokonoe that Hazama knew she was in Yabiko and that Tsubaki was with him. The two straightforwardly talked about their plans, knowing that Tsubaki was likely to kill Noel because of Mind Eater and that Kagura may have to kill Tsubaki if it came to it. Makoto had overheard their conversation and burst in, although Kokonoe reminded her that there were friends on both sides of the conflict. As Makoto left, Tager entered, and Kokonoe ordered that he capture both Makoto and Noel. Kagura was confused, but Kokonoe had already seen on Makoto's face that she intended on finding Tsubaki and leaving the shelter that Kagura was providing. Kokonoe later left with Celica, introducing her aunt to Kagura. When Tager came into contact with Ragna, Kokonoe called the Grim Reaper, letting him know that Tsubaki was in Ikaruga and that she had a good look at the corruption of the Azure Grimoire when she gave him his new arm.
Kagura captured Ragna and threw him into a cell, and Kokonoe spent some of her time gleefully teasing him, telling the Grim Reaper that she never expected to see him behind bars. Putting Ragna in the basement had two purposes for Kokonoe – to make him calm down, and to get him away from Izanami's phenomenon intervention. Kagura revealed that he had known Makoto's location, leading to Kokonoe's frustration in not knowing, having wasted time with deploying Tager. When Jin entered the room with Hibiki, the four of them detailed a plan to use the Colosseum to lure Tsubaki.
She visited Ragna's cell again to listen to Rachel tell the story of The World. When everyone except Celica had left, she told Ragna that she had attached a Multi-Dimension Bomb to his person at a cellular level, and that the only way to not detonate it was to stay by Celica's side. This greatly annoyed him and she reminded him that she could detonate it at any time. She was also present in Kagura's office when Jin and Ragna began to butt heads, and left before it became too rowdy.
The following day, Kokonoe was present at the large meal that was cooked by Hibiki; she was disappointed by the lack of silvervine candy and convinced Noel to start eating. Kagura gave another presentation on the plan that was going to happen the following day, and Kokonoe explained about the Eclipse Field that would be generated to stop Izanami's interference. Later that evening, Arakune attacked the NOL branch and Kokonoe had to explain to them all that only Arakune could enter the NOL building since she was his Observer. Although this shocked everyone, all she could do was apologize, and told them that she would set up specific measures against him.
The following day, Kokonoe did not sense Hazama or Terumi near the Battle of Ragna the Bloodedge, and continued to work throughout the tournament to ensure security and their plans for both Azrael and Tsubaki would work. The Mad Dog entered the arena, but Kokonoe was not ready to send him to the dimensional prison yet, and needed time to prepare. After Kagura and Ragna bought the time for her, she teleported Azrael to Tager's location, allowing him to slug his nemesis before teleporting the Mad Dog to the dimensional prison, sealing him away. She then set up the Eclipse Field to trap Tsubaki and the plan to free her from Izanami was successful.
Kokonoe caught Terumi in the act of attacking Ragna near the edge of the Colosseum and intervened, finally meeting her mother's murderer eye-to-eye for the first time in years. She taunted him, telling the God that humans were finally at their level. Unfortunately for her, Phantom teleported Terumi away, although Kokonoe did not seem to recognize her mother. Later on, she told Ragna about Celica's power to nullify seithr and that she was the key to Kushinada's Lynchpin.
The next day, Kokonoe was startled when Ragna came into Kagura's office and told her that he knew about the method to activate the Lynchpin and how Celica had to be sacrificed for it to work. Kokonoe made her feelings aware to Ragna that it was something that had to be done and was a necessary evil that she had to commit in order to kill Terumi and save the world from Izanami. Their conversation devolved into an argument quickly, leading Ragna to hold her up by the collar; still, Kokonoe stood her ground, she knew Celica's sacrifice was the only way forward.
Rachel interrupted this moment and made the group aware that Tenjo held onto the Lynchpin even without Celica being in the timeline. She then told the group that there was likely another way to activate it, and they all deduced that the Phoenix: Rettenjo was the way to do so since it held Tenjo's noble soul, and that Nine likely modified the Lynchpin so that they could be accepted as a catalyst instead. Despite this, Kokonoe insisted that Celica was still insurance and left the room after asking Rachel who's side she is on. She went to her lab and did some checks on Minerva before deploying Tager to help in the mission to activate Kushinada's Lynchpin.
The second that Minerva arrived, Kokonoe made her objective to protect Celica. She bore witness to the Gigant: Take-Mikazuchi being summoned back to the planet and was shocked to see it. Kokonoe told Ragna that she would have no choice but unleash Celica's limiter so they could have a chance at fighting it, but gave them only 10 minutes to do so before Celica would disappear. Hakumen followed her orders to destroy the Monolith where the souls of the world were being gathered. Bang was successful and the Lynchpin was activated, stopping the flow of seithr across the world, and Kokonoe watched on as Ragna defeated Nu and Take-Mikazuchi, but was sent berserk by Izanami.
To find Ragna, Kokonoe deployed Tager, but she was not hopeful, believing that he had likely died. She later told Kagura and Hibiki that, according to Rachel, the black sphere in the sky was called the Embryo, although she knew nothing about it except its mass, which weighed close to zero. Kokonoe also told Kagura that she could intervene on the Master Unit because the Tsukuyomi Unit was protecting it.
Having directed Tager to return to base with both Makoto and Noel in tow, Kokonoe began to reflect on Lotte and Litchi, thinking that she was not blessed with apprentices. The Committee ordered its soldiers to storm her lab, and they surrounded her. Instead of allowing herself to be captured, Kokonoe escaped, activating a myriad of traps around her to confuse the soldiers. Kokonoe forced the doors around her facility to close, but as she turned, she saw Azrael right in front of her. Both surprised and angry at the fact that someone released him from the Dog House, she launched her Broken Bunker attack toward him, using the smoke from the explosion to mask her mechanically teleporting away.
She arrived in a forest within Sector Seven's territory. Contacting Tager, she warned him to head straight to Yabiko instead of the main base, and then contacted Kagura. She asked for his assistance and was forced to make a trip that would take a human two days' worth of walking distance in order to be picked up by his extraction squad. She organized for Celica to be sent to Yabiko within a large package shaped like a coffin. When she finally arrived in Yabiko, she told Celica that she would have her out by the afternoon.
At some unknown point, together with Celica, Kokonoe went to the church. She left Celica alone with her grave and went to visit the church itself before rushing back when she felt a dangerous presence. Celica told her that the Imperator had visited, and Kokonoe realised that the enemy had learned of the ace that she had been saving. When she returned, Hibiki Kohaku lectured her, although Kokonoe later confessed that Hibiki's talents were wasted as Kagura's assistant and handed Celica to Makoto, who had only just arrived. She ordered the girl to take her aunt across Yabiko, although she was not to let her out of her sights. When she returned to Kagura's office, the two talked about their plan to take down Izanami, Terumi, and Relius.  She later told both Hibiki and Kagura that Izanami's intervention had begun and that they would need to be wary since things would become unpredictable.
Tager and Makoto discovered that Relius' assistant was actually Litchi. When they caught up to her, Kokonoe was able to call her former assistant and denied helping her in saving Roy with Observation. Although this infuriated Litchi, Kokonoe changed her mind after Tager tried to apprehend her. She was in the same room as Hibiki and Kagura when this call went through and reminded them both that the Imperator must know about their rebellion because of the interventions. Kokonoe soon received another call from Tager, this time because he and Litchi were pinned between Nu and Azrael. She mechanically teleported Kagura to their location and had Tager prepare to mechanically teleport the three of them back into the NOL office. This was successful, although she was initially left worried. Litchi told Kokonoe and Kagura about her plan to use an overdrive, observation, and the Azure Grimoire to save Roy, but the professor rejected it because it was far too dangerous for the Observer. She then had Kagura help carry Tager into the basement since he needed to recharge. She overheard a conversation between Makoto and Litchi later that evening, and told them both that the outlook for Ikaruga was not looking good.
Together with Litchi, Kagura, and Makoto, Kokonoe ran to the ruins of the 5th Hierarchical City of Ibukido. She deduced that Relius was attempting to make a Black Beast. When they entered the Grave Marker of Bases, also finding Bullet and Bang Shishigami, her suspicions were correct. She told the latter two about the true purpose of the Ikaruga Civil War, but still could not believe that Relius was going to attempt to create another Black Beast with Arakune as the foundation.
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.
Act 1: Phantom of Labyrinth
|Stage 3: Celica A. Mercury|
Hanging Gardens -After-
Celica: Hm... that's odd. Where'd everyone go?
Kokonoe: Sheesh, there you are... I've been looking for you, Celica A. Mercury.
Celica: Miss Kokonoe! Thank goodness I found someone I know!
Kokonoe: What...? You know me?
Celica: Huh? Of course I know you. You've helped me out so much.
Kokonoe: ...A rather odd story. But it looks like you're telling the truth. Which can only mean I must have called Celica to this timeline... but why do I not have those memories?
Celica: Umm... Miss Kokonoe, are you alright?
Kokonoe: I need to know the truth. Sorry, but you're coming with me to my lab.
Celica: Huh!? Minerva...!?
Celica: N-Now just wait a sec--!
Kokonoe: That doll... did I help create it? It's unthinkable that I would not remember something of such importance... what is affecting us? Is this an intervention? It seems Celica has memories that I don't... but what about the others? Besides, what does this person want by altering my memories? Damn... I need more information. I guess it's time to find the one with answers.
|Stage 6: Rachel Alucard|
Rachel: ...Long time no see, Kokonoe.
Kokonoe: Rachel... What do you want?
Rachel: Nothing in particular. Except for you to stay out of my way. Interesting events are about to unfold. And I am here to see them through.
Kokonoe: I've no idea what happened to you, but it looks like you're pretty weak. Whatever's going on around here took quite the toll on you.
Rachel: ...Have you realized the source of this disturbance?
Kokonoe: Only in theory, but there's one way to find out. I'm going to the cauldron.
Rachel: How unfortunate. You see, I can't have you stand in their way.
Kokonoe: How could you be so weak...? What the hell did you do!?
Rachel: That is irrelevant to you.
Kokonoe: I am only after the Sixth Hero, Hakumen. Right now, the Grim Reaper and Azure Grimoire are meaningless to me.
Rachel: For now... Why not go and see for yourself... ...But let me warn you, you must be prepared to face your own past.
|Stage 7: Hakumen|
the Gate -Not Possible-
Kokonoe: We finally meet, Hakumen.
Hakumen: The Grimalkin... What do YOU want, now of all times?
Kokonoe: Heh, it's beginning to make sense. Of course, the Susano'o Unit would be able to elude the effects of this... field. Let me ask you, Hakumen. Who was it that salvaged you from the Boundary?
Kokonoe: As I thought. Your silence speaks louder than words.
Hakumen: Then we are done here. Leave.
Kokonoe: That's not happening. I need you to tell me EVERYTHING you know.
Kokonoe: Answer me, Hakumen! Who built this world!? What happened here!?
Hakumen: I have no obligation to answer you. Besides... You already have the answer to that question.
Kokonoe: What...!? Don't tell me... How did I not see it...? Of cousre--! My back-up inside the Boundary was still alive... Which means this world is--
Nine: Ah. Ah. Ah. Not yet. Not now.
Nine: Oh, how I wanted to see you, Kokonoe. How you've grown...
Kokonoe: Impossible! How can you be here, Mother!? You fell into the Boundary...!
Nine: You should be able to tell whether or not I'm real. From one mage to another... You can see the flow of magic.
Nine: No need to be so on-guard. I just want you to fulfill your dream.
Kokonoe: My... dream?
Nine: That's right, Kokonoe. I want to see if you have the right... ...To turn it into reality.
|Stage 8: Nine the Phantom|
Nine: Hehe. You are indeed my daughter.
Kokonoe: Then you really are my mother...!
Nine: You musn't. No matter how much hatred you eliminate, you cannot reach that man. You cannot reach Yuuki Terumi.
Nine: With the incorrect sequence, Terumi cannot be defeated. That is why I will tell you the only way you can defeat that man...
Kokonoe: A way to defeat... Terumi?
Nine: Before the Day of Reckoning, the Imperator...No-- Izanami must be defeated. By your hands.
Act 2: Nightmare Memory
|Stage 3: Kagura Mutsuki|
Kokonoe: You were in Yabiko after all... I saw a few others in Ikaruga, so I had a hunch.
Kagura: Were you teleported here, too? Heh, but who could pull off something this insane. You think it's...?
Kokonoe: Yes. I've seen it with my own eyes. There's no mistaking it.
Kokonoe: But right now, I've got a favor to ask you.
Kagura: Whoa, before that... Answer my question.
Kagura: I hope you didn't forget about out little encounter in Kagutsuchi? Where you held me back. I need to know one thing, Kokonoe. Are you on my side or not?
Kokonoe: If those are my only two options, then I'm afraid it is neither. Let's say, though, I were your enemey... What would that change?
Kagura: For starters... I'll need to remove you from the picture, unfortunately.
Kokonoe: My goodness... I've put up with your little side show. Haven't you had enough?
Kagura: Heh, you already noticed...?
Kokonoe: We are neither friend nor foe. We are simply working together as long as our interests are aligned. Surely, you know what this means.
Kagura: Fair enough... But Kokonoe, how do you see this situation?
Kokonoe: It's likely that this world and all of our memories are fabricated.
Kagura: All of us? At the same time? Who could possibly pull off something like that?
Kokonoe: I've got a pretty good hunch... But I need to assess the situation before jumping to conclusions. Why do you think I'm here? Kagura, you take a look into the others. Give me any information on Izanami, ASAP.
Kagura: What are you going to do?
Kokonoe: ...Search for Noel Vermillion.
|Stage 6: Arakune|
Arakune: Kihe... Hehehe! I've fou..d you. Koko...e!
Kokonoe: Roy... You're here too... But something's different from before?
Arakune: Teleportati..n ...agic. You are... Ni...e's ...aughter, yet hidd...n yo... agic! Why!?
Kokonoe: Impossible...! You've absorbed a Nox Nyctores!?
Arakune: Kiheheheheh! I will... abs...rb you for know...ge!
Arakune: G'gyah! Why you... Koko...e! Not ...et. Still need Nox... ectores!
Kokonoe: Why do you need them!?
Arakune: Obvi...s. Koko..e. To surpa... ou! Kiheheheh!
Kokonoe: It couldn't be... He's already noticed? All the more reason I can't let him have the Azure... Damn, I need to hurry!
|Stage 7: Relius Clover|
Kokonoe: You're... Relius Clover!?
Relius: ...Ah. Kokonoe.
Kokonoe: The fact that you're here... must mean you are at least tangentially involved in our little... incident.
Kokonoe: I think I already know the answer, but did you tell Roy about the Nox Nyctores?
Relius: I realize you're under the influence of the Embryo, but you've really become a boring soul, Kokonoe.
Relius: ...Of course. This is all caused by you encountering Nine. Don't disappoint me.
Kokonoe: Heh. I appreciate the concern, but I've noticed the irregularities ages ago. In fact, how about I prove it right now? You can see what's changed in my soul for yourself!
Relius: Mmm... It would appear you are indeed much stronger than I remember. Carl's rage has taken a rather dull turn; however... It seems to have had a much different effect on you. Most interesting. I take back what I said earlier.
Kokonoe: I don't give a damn about that. I've got questions for you. What did you mean when you said the Master Unit doesn't exist in our world?
Relius: That question should answer itself, momentarily.
Relius: It means the opening act is finally over, Kokonoe!
|Stage 8: Izanami|
Sight of Gods
Izanami: Hehe... Kokonoe. To think you're the one to arrive, at this stage, no less...
Kokonoe: Pathetic... This is what the Embryo is supposed to be? You done pretending to be the Imperator, Izanami?
Izanami: My goal is all but fulfilled... The position of Imperator was no longer useful to me.
Kokonoe: Goal...? You mean summoning the Master Unit?
Izanami: I think you're misunderstanding something. The Master Unit has always been here... Quite simply, no one has been able to see it. Now, the Embryo will begin to aggregate. Then my design will be complete! Though, i suppose I owe you a chance to make your dream come true, as well.
Kokonoe: ...What are you talking about?
Izanami: You wish to kill Terumi, do you not? Then the Azure will prove imperative to your mission. Defeat me, and I shall bestow upon you its fragment.
Kokonoe: Hmph... Either way, I have no intent of letting you roam free. While I'm at it, I may as well have you cough up information on the Embryo.
Izanami: Your strength is impressive. I see that you do in fact have the right to hold the Azure.
Kokonoe: Sorry, but I've got no plans for the Azure. I've seen enough people lose their minds trying to chase it.
Izanami: Such arrogance... I should have expected as much from Nine's daughter.
Kokonoe: Huh, don't make me laugh. You've got her under your control right now.
Izanami: Oh? Were you not aware? Nine is no longer under my domination.
Izanami: Was I not clear? The Phantom's curse has already been lifted...
Kokonoe: How could this...? Then you mean Mother is...!?
Izanami: I'm sure you must be aware of why. Why one of the Six Heroes, Nine would have reason to loathe the gods.
Izanami: She has been denied by the world itself... Sounds like enough to draw one's blade toward the gods. Doesn't it?
Kokonoe: Gods...the Master Unit...?
Izanami: Correct. The Master Unit is the source of...all phenomena in this world.
Izanami: Killing it, would be Nine's only desire.
Act 3: The Replacement Blue
|Stage 3: Arakune|
Arakune: Wh... are you... here, Koko...e!? I cannot... su...pass you without... Get out of... way!
Kokonoe: Roy. Why are you here? The readings I saw were definitely that of Murakumo... Don't tell me, you've fused with it!?
Arakune: Kihe... hehehe... Yo...ve real...zed, Ko...noe. What you... se...k is in...de of me!
Kokonoe: Impossible... You couldn't have consumed a Nox Nyctores. Roy, what the hell are you trying to become...!?
Arakune: Hehehe... No know...dge of Boun...ary. You don...t kn...w. I will eli...nate Noel Vermi...lion!
Kokonoe: Noel Vermillion!? Of course... Then I also have a pretty good idea who put you up to this. But too bad... Consume the Nox Nyctores or not, you'll never reach the Azure. Ever.
Arakune: Shut up! I will acq...re and sur...ass you! Do...t dare sta...d in my way!
Arakune: Gyaaaaah! Pain pain pain pain... Koko...noe...!
Kokonoe: ... Binding a soul... Use that to your advantage, and you can even kill the Successor to the Azure... Which means...a phenomena weapon, or Kushinada's Lynchpin could make killing Noel Vermillion possible. Mother most likely created the phenomena weapon with the Lynchpin as its foundation... Then what about...? What are you trying to do, Mother?
|Stage 6: Makoto Nanaya|
Kokonoe: Makoto? Why haven't you checked in like you were supposed to?
Makoto: I tried to many times, but I couldn't get through...
Kokonoe: Right... Probably has something to do with recognition being distorted. But never mind that right now... Have you seen Noel Vermillion?
Makoto: No. I'm actually searching for her right now, too... Why are you searching for Noel?
Kokonoe: I see... It has nothing to do with you. Forget we had this conversation.
Makoto: Don't tell me you're after Noel, too, Professor!?
Makoto: I knew it...Everyone's after her in this world. But I'll protect her, no matter who I'm up against! Don't you dare lay a finger on my friend!
Kokonoe: Settle down, you idiot!
Kokonoe: I never said anything about laying a finger on her. I want to protect her...
Makoto: Whaaa!? Well, you should've said something sooner...
Kokonoe: You said something about me being after her too. Who else do you know is after Noel right now?
Makoto: The ones I've seen... Carl, Major Kisaragi, and some guy people called the Mad Dog... Azrael, and... oh yeah, Relius Clover.
Kokonoe: That damn monster is after her, too... This is gonna be more trouble than I thought... Good work. Rendezvous with Tager and collect more Nox Nyctores.
Makoto: You're not coming with, Professor?
Kokonoe: I'm leaving that up to you guys... I need to find Noel Vermillion, ASAP.
|Stage 7: Noel Vermillion|
Kokonoe: Though I'd find you here...
Kokonoe: I see... You've been hiding from the others here... I'm sorry, I don't have time for sympathy... I don't have time for a lot of things right now. So, I'm going to cut right to the chase... I need to see something with my own eyes. ...What exactly are you to this world?
Noel: *pant pant*
Kokonoe: This reaction... You really ARE the core to the Master Unit.
Noel: Master... Unit?
Kokonoe: ...Huh? Wait... What happened to Kusanagi!?
Noel: Kusanagi...? Who are you?
Kokonoe: Your memory isn't back... What's going on!? When the Master Unit showed itself in the Embryo, it should have merged all memories... Don't tell me...! You released Kusanagi along with your own memories, Noel!? Then what the hell did you... What did you see inside Ragna the Bloodedge...!?
Nine: ...Your conversation has piqued my interest.
|Stage 8: Nine the Phantom|
Nine: Aww, you don't call me Mother anymore? That just makes me sad, Kokonoe.
Kokonoe: You're an ancient relic that should've died in the past... I ask you don't meddle in the affairs of the present.
Nine: Heh heh... Your eyes are terrifying. You are definitely my daughter. But... I'm afraid I can't honor your request.
Kokonoe: In other words... You intend to kill Noel Vermillion?
Nine: You're a clever girl... You know the pain I must be feeling. This pathetic predestined path will never change as long as she exists.
Kokonoe: I do understand your frustration and anger... You even have my sympathy. Nonetheless, I will NOT permit you to kill Noel Vermillion! Get behind me, Noel!
Kokonoe: Tch! Why do you insist on killing Noel Vermillion!?
Nine: I already told you my reason... There's no reason to prolong this chat.
Kokonoe: You should be aware of the repercussions when you kill her. This isn't some simple reorganization... Are you trying to destroy this whole world!?
Nine: I have countermeasures in place. I like to call it the 11th...
Kokonoe: Don't tell me...that replica!?
Nine: ...I'm amazed... You actually found it. I should be commending you... my daughter.
Kokonoe: Countermeasure or not... ...You want to deny the present and pull us all back to the past... ...I don't accept what you are trying to do!
Nine: It is rather unfortunate.
Kokonoe: Those in the present have the right... ...to decide their fate.
Nine: I think I understand how you think. You know what this means, Kokonoe... As of right now... ...We are mortal enemies.
Kokonoe: ... Don't worry, Noel Vermillion. I will protect you from Nine.
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: Phase Shift 4, Chapter – Colorless Guiding Light
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Story Mode, Episode 04: Kagura Mutsuki
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 6: Friendship
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 7: Ragna, The Wanderer
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 9: Izayoi
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 11: The Night Before…”
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 12: Uninvited Guest
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 13: Mad Dog
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 14: Inherited Will
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 15: The Truth
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 16: Kushinada's Lynchpin
- BlazBlue: Chrono Phantasma, Story Mode, Chrono Phantasma, Episode 17: Doomsday
- BlazBlue: Chrono Phantasma, Story Mode, Episode 18: Beginning of the End
- BlazBlue: Chrono Phantasma, Story Mode, Epilogue
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 1: Wrong Place, Wrong Time
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 2: Unwavering Feelings
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 3: The Melancholy of Celica
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 4: The Land of Ikaruga
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 6: Litchi's Determination
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 7: Looming Darkness
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 8: The Forbidden Research
- BlazBlue: Chrono Phantasma, Story Mode, Sector Seven, Episode 9: The Beast
- 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
|Other (C-series)||Edgar and Claire Vermillion ·Ellen Nelson · Four · Francis and Rosenne · Lao Jiu · Pakumen & Terumen · Three · Two|
|Remix Heart||Elina · Guardian ·|
|Variable Heart||Julian ·|
|Alternative: Dark War|
|Persona 4 Arena/
|Under Night In-Birth|