For reasons unknown, Rei was inside a Phantom Field, specifically one created by Trinity Glassfille. Within this Field, which was set within the Magister's City of Ishana prior to the Dark War, Rei's memories were altered to make them believe that they were a student of the Mage's Guild. A version of Kazuma Kval was also present in this field, who was supposed to guide Rei across the island.
Rei was seemingly a transfer into the Mage's Guild. They could see a being known as the Red Sentinel - Kazuma believed this to be an indicator that Rei had tremendous magical power, despite reality being the opposite. Trinity joined in on the conversation, remarking that even Konoe A. Mercury and the Ten Sages had difficulty being able to see the Red Sentinel. Kazuma and Trinity continued working on the robes for Konoe's Canonization Ceremony, but then Rei saw the Sentinel in a hallway and gave chase. They ended up near the cauldron, which Rei recognized. The Red Sentinel began to speak, and asked that Rei not lose. Rei was then moved to a forest where they interrupted a battle against Another Dark Mai and Ciel Sulfur. Mai took notice and went to kill Rei, but at that moment, Phenomenon Intervention occurred. Mai was distracted, so Ciel took Rei away from the fight.
Rei lost consciousness. They began to dream, seeing Ciel, who introduced herself and promised to protect them. Rei awoke, finding Ciel next to them. Kazuma ran over to the both of them, asking where Rei had been, and becoming increasingly alarmed as monsters began to swarm around the trio. Rei stood back, as they are unable to fight, while both Ciel and Kazuma fought against the surrounding beasts. As the battle ended, Ciel called out to Rei, referring to them as an Observer.
Moments later Another Dark Mai arrived. Rei appeared to recognize her, but did not know where from. Kazuma and Ciel's noisy conversation about whether to engage against Mai lead to her turning her attention towards them. Mai did not take well to being called an enemy, and introduced herself as a "villain" who was going to stab Rei again and again. Rei then began to slightly break down, but was shaken out of it by Ciel, who asked that they don't Observe Another Dark Mai too closely. Mai then threatened to kill them all again, but the trio were teleported away from her thanks to Raabe, who had used Phenomenon Intervention. Both Rei and Kazuma were shocked by this, but Ciel explained the situation to them both now that they were safe. Ciel continued, telling them both that she belonged to the Mitsurugi Agency, and was not native to Ishana. Together the group decided that, since this Ishana was essentially empty of people, they would try to find the cauldron within Ishana and find a way to solve what was wrong with the island.
As the group headed further into the island, Kazuma explained to Rei about the Mage's Guild and Ishana's history. It was also here that Kazuma pointed out that Rei's uniform was an old design, one that hadn't been used by the Guild in a long time, and that Rei also seemed incapable of using either magic or sorcery. They were then attacked by monsters, but they were fought off due to a combination from Ciel and Rei which they discovered together, allowing them summon Chrono Phantasma (Those Who Should Not Exist) as embodied units to fight alongside themselves. The group then decided to head north-east towards an Ishanan port to find a communications device in order to see who else might be on the island. When they eventually arrived, they did not find a working device, but instead were met by a piercing scream in the distance. Rei went to run over with Kazuma, but was held by by Ciel. Rei explained that they couldn't just sit back and let someone get hurt. Rei convinced Ciel to come with them.
The group then fought through waves of monsters, with Rei using summoned units to help. They finally made their way through, finding Trinity Glassfille. She told them that Ishana's barrier had disappeared and that a secondary defence system had likely activated in order to isolate the island within another dimension. The group decided that the Great Library was likely the one place that would have information on how to save Ishana from its predicament. On Trinity's suggestion, the group went through the sewers to reach the library while avoiding detection, but were attacked by more monsters. When they made their way out of the sewers and into a park, they were attacked again. The island was swarming with monsters that were attracted to Ciel and seemingly Rei as well. The monsters were defeated and the group made their way further towards the library, walking past the Grand Clock. Rei noticed that the time on it had not changed, yet to Trinity, the time was indeed different.
Finally inside the Great Library, Trinity made it clear that they were going to have to fight a security system in order to enter a forbidden section of the library which would contain information they were looking for. After beating the golems summoned by the system, Trinity told them that she was uncomfortable with Ciel entering since she is an outsider, but Ciel stood firm, telling her that she needed to enter in order to protect Rei. Rei and Kazuma reaffirmed their trust in her, eventually persuading Trinity to allow both Ciel and Raabe access to the hallowed sections. Rei helped comb through the numerous books, but it was Ciel who suggested that they find the cauldron once more and deactivate it, thereby taking Ishana out of the secondary security which had placed it within another dimension. Before proceeding, Rei was asked if this plan was okay and they gave it the go ahead. The team then left, making their way to the most sacred of Ishana's destinations where the cauldron likely lay - the Ishana Cathedral.
On their way to the cathedral, Ciel confessed that she was going to destroy the cauldron. Trinity and Kazuma couldn't accept this, but Rei told them that they had no reason to distrust her, eventually persuading both of them that the plan was sound. As they descended through the cathedral towards the cauldron, both Ciel and Kazuma told Trinity that they believed her to be an Observer who had subconsciously recreated Ishana, but they were unable to figure out why Rei had been placed within the Phantom Field alongside Kazuma. More monsters flooded in that the group defeated.
As the group reached the cauldron, they saw Another Dark Mai, who had been waiting for their arrival. She expressed an interest in Rei and Ciel, telling them that she had stayed within the Field because she found them interesting. A battle begun between Dark Mai and the units summoned by Rei and Ciel. Eventually, the dust settled and Dark Mai left via the cauldron. Trinity then turned to the group, unable to accept her position as an Observer and unable to let her desires go. She was battled and defeated. Ciel was then able to activate her BlazBlue Alternative as Rei Observed it, allowing for the cauldron to be destroyed and Trinity to be freed from her Phantom Field. As the Field was beginning to reform into a new Possibility, Ciel took Rei with her and the two came on board of the Dimensional Boundary Submersible Warship Fugaku. When Rei gained an understanding of where they were, they were greeted by Kagami Hajou.
After boarding the Fugaku, Rei was taken for a medical check that was organized by Kagami. She confirmed that they were medically sound and proceeded to introduce herself, the Fugaku, and the Mitsurugi Agency. She then explained that they were inside the Boundary, sailing through it in order to find the various Phantom Fields, the worlds that should not exist. Kagami further explained to Rei that the Ishana they were in was a Phantom Field that had reset 182 times, and that it was created by Trinity's own desires. In order to save the Observers who are trapped within their Phantom Fields, the cauldron within the Field had to be destroyed.
Kagami further explained to Rei that she had no idea how they were in the Phantom Field and that they were not magically strong enough to be admitted to Ishana. She asked them to join the Agency in freeing the trapped Observers. As well as this, she confirmed to Rei that they had a Drive which was the ability to Observe at an unprecedented level. This Drive was named End Gazer and Rei listened as Kagami explained what a Drive is. Ciel interrupted Kagami as she was trying to force Rei to help them. Kagami introduced Rei to the Takamagahara System which was controlling the Fugaku and asked that they think about the offer to join them. Rei was then escorted by Ciel back to their room, where she thanked them for their help in Ishana. She confessed that without Rei, she had difficulty operating the BlazBlue Alternative and left afterwards.
The following day, Rei confirmed to Kagami that they wanted to help. With Ciel and Raabe, Rei dived into the new Phantom Field. In the Field, Raabe introduced itself as it was fixed and able to speak. It explained that it is based on Kagami's personality and would help guide them in the Fields. Rei listened as Ciel and Raabe discussed the way that they could identify the Observer in this Field, eventually concluding that they would have a Drive and would also subconsciously avoid the cauldron. With this in mind, the three of them began their search. Ciel left to do reconnaissance, leaving Rei and Raabe alone. Raabe told Rei that they would need to prioritise their own survival and that Ciel was many times stronger than they are. Ciel soon returned and explained that they would need to fight through monsters made of seithr in order to reach a nearby village.
When they arrived at the village, the villagers were wary, believing them to be from the Novus Orbis Librarium. Before much more could happen, the NOL surrounded them, believing that the group was part of a local resistance. Rei, Ciel, and Raabe fought back defeating the guards. A version of Tsubaki Yayoi then appeared and, after having rallied the soldiers together, was able to detain Rei, Raabe, and Ciel.  They were detained in a cell within the 17th Hierarchical City of Yamatsumi, where Tsubaki began to interrogate them. This interrogation was cut short as she realized that they were unfamiliar with the world around them. Instead she explained the NOL and the concept of a Hierarchical City to them. Tsubaki soon left afterwards. Rei listened as Ciel and Raabe decided to aid the resistance so they could learn more about the Phantom Field, thereby helping to identify the Observer. They were interrupted by a woman in another cell, who picked up on the group not being from this world. An explosion rang throughout the building as resistance members flooded into the prison to rescue the woman in the cell – Bullet, the resistance leader. The rescue was headed by Kuon Glamred Stroheim, and together the resistance and the trio were able to escape. 
The NOL gave chase. Rei, Ciel, Raabe, Bullet, and Kuon stuck together to distract the NOL from other resistance members who were freed. They fought against a security golem, besting it.  Finally escaping from Yamatsumi, Bullet offered the group the chance to join her and the resistance in taking down the NOL. This invitation was turned down, and instead Bullet told them of an inn outside of the Hierarchical City that they could stay out. They said their goodbyes and, while walking to the inn, Kuon confided in them that she was a Contaminant, similar to the group. She recognized Rei's attire as an old Ishanan uniform. Eventually they arrived at the village with the inn, and were finally able to sleep.  The following morning, they listened to the villagers impressions of both the resistance and NOL before leaving for another village. 
In the next village, the group found it was being attacked by monsters while being defended by Bullet. They came to her aid, managing to stop any casualties from occurring. Bullet agreed to help them over to the next village. On the way to the next village, the group destroyed various monsters which were blocking the path.  In that village, it was apparent that Bullet was loved and adored by the people there, and she revealed that she is fighting for her pride. Bullet promised them that she would help them as much as possible. Bullet later gave a mission to Ciel, Rei, Raabe, and Kuon: infiltrate Yamatsumi to rescue a trapped resistance member. They agreed to take on the mission and infiltrated the city without incident.
The group soon found the agent and agreed to escort him out in the fight through the sewer system. Raabe stayed behind to guard the agent while Rei, Ciel, and Kuon went for lunch and to gather information. Hoodlums approached them after their meal, but Kuon soundly defeated them using explosive magic. This, however, attracted NOL guards to their position. The guards, oddly, let them go, rousing suspicion in Ciel and Kuon. When the night approached, the group went to the sewers, but were discovered by patrolling guards. With no choice, the group fought through them.
The sewers were filled with demons, which the group were forced to fight through. After fighting through hoards of monsters, Raabe and Kuon discussed how unusual the NOL was acting. Despite being on high alert for resistance members, the entrance into Yamatsumi had been easy and the guards did not care much for Kuon's explosive fight earlier that day. They were interrupted by Ripper, who had suddenly appeared to attack them. Rei was shoved aside by Ciel for this fight as Ripper landed deep blows on the agent, Kuon, and a shallow slash on Ciel. The fight was going badly for the group until Bullet arrived with backup; Ripper left in response to her arrival.
Bullet escorted the group back to a village where they could recover. Ciel, Rei, and Raabe decided that they would be going to investigate the NOL within Yamatsumi. Kuon stopped them, telling them that she would be joining as she felt responsible for Ripper since they were from the same Possibility. They made their way to the higher levels of Yamatsumi to get a better understanding of the city, but they were almost immediately spotted by Tsubaki and the NOL guards surrounding her. The guards attacked the group, but Tsubaki interrupted them, dismissing the guards. Raabe offered to give her information about the resistance so long as they could talk in private. Tsubaki agreed. They moved to a more private area, where Tsubaki asked them to be mediators between herself and the resistance. Jin Kisaragi would be arriving in Yamatsumi soon with reinforcements to continue building and managing the city, and they were going to destroy the resistance as well. The group agreed to help as mediators to avoid bloodshed. 
As the group came back down Yamatsumi to return to the village, they were about to be attacked by Ripper. Ciel, Raabe, and Kuon asked him who was ordering him to attack them, but he declined to answer, instead sharpening his blades and attacking them. Tsubaki interrupted the fight, forcing Ripper to flee once more. She handed a communicator to the group as they explained that Ripper had been killing resistance agents, meaning that negotiations were unlikely to go well. Regardless, they agreed to continue to act as mediators. They continued their way back to the village but found Bullet and other resistance members in the middle of a raid. They learned she was going to steal a mechanical shaft that was essential to the development of Yamatsumi. They extended the offer for negotiations that Tsubaki wanted, but Bullet declined, telling them that she would never join the NOL nor would she allow them to continue to do as they please. To prevent them from leaking the raid to Tsubaki, Bullet ordered that the resistance members apprehend the group, but they were powerless to do so.
Ciel called Tsubaki and alerted her to the raid. Tsubaki relayed that those parts had already arrived. and that Bullet had likely been given false information. The raid would instead be on a civilian ship which could lead to fatal casualties. Tsubaki reunited with Rei, Raabe, Ciel, and Kuon and also made her aware that Bullet had declined their peace offering. Before they could act to stop her, they were interrupted by Hibiki Kohaku. He told the group they were under arrest as they had broken from the jail they were confined to earlier. After a fight, Tsubaki ordered the group to leave and stop the resistance while she held off Hibiki.  They caught up to Bullet and helped her escape from the NOL after telling her and the resistance that they had been set up. When they returned to the village, the group found it was destroyed with scores of dead bodies. Ripper had destroyed it and killed as many people as he took pleasure in doing so. Bullet swore revenge on the NOL, knowing that this order must have come from Hibiki Kohaku. She rallied everyone together and ordered that they would destroy the mechanical shaft. Kuon, Ciel, Raabe, and Rei pleaded with her to reconsider, but these pleas fell on deaf ears. The group decided that they needed to see Tsubaki. 
The following morning, Kuon, Raabe, Rei, and Ciel were surrounded by the resistance, weapons raised. The group struggled, hoping to break free, but this ended when Bullet arrived and took Rei hostage. Bullet and other members of the resistance left soon afterwards. With few guards left, the group was able to bust out and free Rei. As the group made their way towards Yamatsumi, Raabe called Tsubaki and made her aware of what Bullet was aiming to do, and also told her about the massacre that Ripper had enacted upon the village. Tsubaki told them that the shaft the resistance was targeting was essential to Yamatsumi's infrastructure. Without it, the city would collapse. They were able to reunite with her and a group of NOL soldiers loyal to her. The group ventured deeper into the NOL branch, finding no guards protecting the perimeter. Tsubaki noted that the soldiers were likely being led by Hibiki and battling the resistance on a higher level. They accidentally activated a security golem but were able to destroy it before proceeding.  Ripper then appeared, confessing to the slaughter of the villagers. The group battled against him, managing to defeat him and forcing his retreat. Ciel and Raabe made the decision that they would have to push forward to find Hibiki and Bullet before it was too late.
When they finally found them, the two were locked in battle while soldiers from the NOL and the resistance lay nearby. Tsubaki pleaded with them both, begging the violence to stop with a passionate speech that resonated with the nearby soldiers. They pleaded with Bullet to stop the violence but she refused and the Phantom Field began to rewind back to before the soldiers agreed with Tsubaki. Now they turned against her; Kuon, Ciel, Rei, and Raabe defeated these soldiers.  Reinforcements came to back up Bullet and it was then that Ciel and Raabe knew that Bullet was the Observer of the Phantom Field. They were able to conclude that all she wanted to do was to fight forever, and that any attempts to stop it would always be prevented. Peace or victory were never options, only violence. Ciel was then able to confirm the presence of a cauldron and explained that they could destroy it to free the field. Hibiki sided with the group, but Bullet then began to attack, not letting them take away the only thing she had ever known – violence. Monsters flooded in, generated by the Phantom Field to exterminate the group. 
The Phantom Field then began to operate to continue the battle forever, something that Bullet could not even control. Hibiki, under the Observation of the Field, changed sides to fight alongside Bullet, and the two attacked with combined forces from the NOL and the resistance. Bullet's Observation then focused on Tsubaki as it tried to make her hostile towards the group. Tsubaki tried fighting back, but it was a losing battle until the arrival of Jin Kisaragi. He demanded that Tsubaki move to the backline while he stood with Ciel, Rei, Raabe, and Kuon to fight against Bullet.  The group was able to defeat Bullet, something which she accepted. Jin stayed behind to look after Hibiki as everyone else went down to the cauldron. They said their goodbyes as Ciel destroyed it, allowing Rei, Raabe, and Ciel to return to the Fugaku. On board the ship, Kagami congratulated them on the job, but Ciel insisted that Rei get some sleep. Later on, both Rei and Ciel enjoyed some tea together.
- BlazBlue Alternative: Dark War, Prologue, 1
- BlazBlue Alternative: Dark War, Prologue, 2
- BlazBlue Alternative: Dark War, Prologue, 3 - 1
- BlazBlue Alternative: Dark War, Prologue, 3 - 2
- BlazBlue Alternative: Dark War, Prologue, 3 - 4
- BlazBlue Alternative: Dark War, Prologue, 4 - 1
- BlazBlue Alternative: Dark War, Prologue, 4 - 2
- BlazBlue Alternative: Dark War, Prologue 5 - 1
- BlazBlue Alternative: Dark War, Prologue 5 - 2
- BlazBlue Alternative: Dark War, Prologue 5 - 3
- BlazBlue Alternative: Dark War, Prologue 6 - 1
- BlazBlue Alternative: Dark War, Prologue 6 - 2
- BlazBlue Alternative: Dark War, Prologue 7 - 1
- BlazBlue Alternative: Dark War, Prologue 7 - 2
- BlazBlue Alternative: Dark War, Prologue 7 - 3
- BlazBlue Alternative: Dark War, Chapter 1, 1 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 1 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 1 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 1 – 4
- BlazBlue Alternative: Dark War, Chapter 1, 2 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 2 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 2 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 2 – 4
- BlazBlue Alternative: Dark War, Chapter 1, 3 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 3 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 3 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 3 – 4
- BlazBlue Alternative: Dark War, Chapter 1, 4 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 4 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 4 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 4 – 4
- BlazBlue Alternative: Dark War, Chapter 1, 5 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 6 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 6 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 6 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 7 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 7 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 7 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 7 – 4
- BlazBlue Alternative: Dark War, Chapter 1, 8 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 8 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 8 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 9 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 9 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 9 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 9 – 4
- BlazBlue Alternative: Dark War, Chapter 1, 11 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 11 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 11 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 12 – 1
- BlazBlue Alternative: Dark War, Chapter 1, 12 – 2
- BlazBlue Alternative: Dark War, Chapter 1, 12 – 3
- BlazBlue Alternative: Dark War, Chapter 1, 12 – 4