Finished the game, decided to write a timeline of events and story summary due to the complexity of the story if people want it. Feel free to correct or add things if I am mistaken.
This is a broad overview based on the events and notes as presented by the game.
Spoilers
Before the events of the game:
in the land of Sakuraba, youkai and samurai were in conflict as youkai would terrorize humans for their sexual essence, leading to samurai killing any youkai they found. However, a mysterious organism landed and began seeking out organic lifeforms. It consumed beasts, birds, fish, and both youkai and humans by turning them into monsters. Both youkai and samurai banded together to defeat this threat known as the Mononoke from spreading its disease. Lead by the lord of Sakuraba, Onma Tadakatsu, with his samurai retainers including the Tachibana and Sakura clan, as well as the the three great youkai. They managed to stop the Mononoke, but not defeat it, with many youkai and samurai losing their lives, including Sakura and Tokuro parents.
Afterwards, the lord of Sakuraba eventually made a deal with the youkai for helping defeat the Mononoke, allowing for youkai to live and work in the region. However this did not mean all was well. The lord retrieved a piece of the surviving Mononoke, called the Mononoke leg, and began researching to either defeat it or find way to tap into the power without sucumbing to its disease. Hanahiru, Kirari's mom and one of the great youkai, grew to fear the samurai as their martial strength could easily hunt down and kill the rest of the youkai if they wanted to. Thus, Hanahiru began formulating a plan to weaken the samurai by feigning alignment with the Sakuraba lord. While she would operate the brothel as a safe space for the youkai, as well as try to gain access to the castle and steal the Monooke research for herself.
During this time, both the Tachibana and Sakura clans continued with Sakura becoming head of her clan and Tokuro his. Tokuro would work to grow in power, taking care of both his sister, Tamago and Sakura who he trained her under his guidance. Had things continued, Tokuro would have gained a promient position under lord Sakuraba. However, he began having relations with Hanahiru, who he did not know was a yokai. When Tokuro met with Hanahiru, he began having feelings for her and decided to make her his wife instead. However, Hanahiru, wanting to use Tokuro to gain access of the castle decided to take his manhood away instead. When Gofu awoke, he grew distraught over his lost due to having his heart broken as well as with his inability to sire any children to continue the tachibana lineage. Thus the tachibana fell into ruin, with gofu disgraced and made to work as a double body guard / assassin and his sister now a spy for the castle.
Timeline 1:
As the timeline continued, the events played out as so. Sakura grows up and wanting to reestablish her family legacy, participate in the martial tournment set up by the lord who wants to use it as a way to find an heir. This is due to the fact that tomo had been secretly poisoning him with a drug to make him unable to have children to prevent him from having his way with her. With no way to produce an heir, the lord needs someone to contue protecting Sakuraba for the return of the Mononoke. In the first match, Sakura duels with Enka who wants to prevent Sakura from become the lord's heir. Unbeknownst to Sakura, the penelty of defeat is death, which Enka is executed after Sakura leaves. Sakura's next duel is against Tokuro, who after failing to despair after all these years decides to either win a chance to restore the Tachibana family or at least die as a true samurai. The battle between them results in Tokuro's eyes being sliced and Sakura's arm being cut off. Before Sakura can make the final blow, Enka's body appears due to Hanahiru and Kirari interference. This results in Sakura becoming enraged and attacking the lord before being subdued. The reasoning appears to both in attempt to have Sakura kill the lord or have Sakura killed, thus preventing a heir. As well as possibly to spare Tokuro.
Seeing this display, the lord believes Sakura is fit to be his heir. The lord tells her of the situation, the Mononoke and the threat it places on the land and why only the strongest can be the future lord. Sakura, after hearing this agree to the cause but due to the lost of her friend begins falling into darkness. After the lord passes away and Sakura become the next lord, her first task was to defeat the Mononoke beast on the Osore pass. It was defeated, but after the lost of Tamago who perished during the attack. On the return home, they were attacked by Hanahiru who saw the opportunity to take the Mononoke beast and raid the castle for the Mononoke leg. However, when Hanahiru got the leg, it began transforming her into a monster that devastated the castle. The newly formed beast began spreading the disease over Sakuraba, leading to it's near destruction. The aftermath was that Sakuraba became a wasteland cut off by the outside world with the youkai retreating and the townsfolk slowly becoming mad. Sakura herself slowly being corrupted by the disease which turned her into a mad lord.
It is in this world which Suzune is born. After losing her parents, she is saved by Tokuro and decided to take her in. He plans on leaving with her, but Suzune is kidnapped by Sakura, as Suzune has an apparent immunity to the disease, meaning she could possible hold the key to a cure to surviving the Mononoke. However Tokuro managed to track down and duels Sakura, only to be defeated taking her with him. In the aftermath, the castle is destroyed, killing Suzune but her soul is saved by Nurari who been watching her and taken a great fondness to the point of adopting her. Feelings her dismay over losing her father figure and the future of sakuraba, Nurariuses her power to send Suzube back to fuffil her two wishes. To create a future where everyone lives happily, and to fufill the wish so Tokuro can die as a samurai. This starts the beginning of the game were suzube finds Tokuro but is adopted as Sakura's disciple.
Timeline 2:
This timeline begins as normal, however with Suzune now with Sakura. the events play out similar up to the tournment where Sakura and Tokuro duel, both mortally wounding each other. However, unlike timeline 1, Kirari is unable to disrupt the duel by dumping the body of Enka and causing Sakura to go beserk at the lord. Resulting in Sakura decapitacing Tokuro's head. This result causes a time loop to occur, as the wish for everyone to live can not happen. This brings Sakura and Suzune back to the beginning of the game to try again.
Timeline 3:
With knowdelge of the future, the events of the timeline changes. Informing Enka of the event, causes her to not join the tournment, saving her from execution. Informing Tamago of the events causes her to drug Tokuro from participating but Tamago decides to take his place for a chance at restoring the Tachibana family. Sakura defeats Tamago but refuses to kill her per the lord's order. Seeing this defiance, the lord challenges Sakura, resulting in her arm being cut off. She is about to be killed until Tokuro intervenes and cuts his eyes out to appease the lord. This works, but Kirari joins in, sent their by her mother to try and kill Sakura to prevent her from becoming the heir, as well as wanting to avenge her sister that Sakura killed. The lord allows this, resulting in Kirari and Sakura battling with Sakura victory. Impressed by her determination and skill, the lord names her the winner. However, despite having saved everyone from dying, the second wish causes another timeloop to happen, sending Suzune, Sakura, Tamago, Enka, and Kirari to the past.
Timeline 4
With everyone having remembered the past experience, they realized that something is keeping them from moving on to the future. They plan on meeting the third great yokai, Kokotsuzumi, who can maniplate memories. After traveling up the mountain and meeting her, they uncover the Susune memories of the original timeline and the destructions of Sakuraba. Unable to fufill both wishes, they plan of taking out the Mononoke research instead to prevent the destruction in the future. They plan on convincing Hanahiru to use her space manipulation ability to let them into the castle undetected, but are betrayed instead, revealing that the destruction of the Mononoke research would ruin her plans on defeating the samurai. Hanahiru is defeated however, and the group are sent to the castle where they make their way to the room where the Mononoke research is being done.
Timeline 4, Ending O
Before the group manages to destroys the research, Hanahiru was waiting to take the Mononoke Leg to use for herself. However, the mononoke leg begins transforming her into the beast of Timeline 1 that destroyed Sakuraba. This time, with Sakura, Enka, Tamago, Kirari, and Suzune in the same proximity, they become trapped with the rest sacrificing themselves and letting Suzune escape before being consumed by monster Hanahiru. Suzune encounters Tokuro whose been blinded by Hanahiru and is knocked out by him. He takes the unconscious Suzune to escape before Sakuraba falls just like in timeline 1.
Timeline 4, Ending B
Before the group manages to destroys the research, Suzune takes the Mononoke Leg before Hanahiru can get it. But Hanahiru kidnaps Suzune with the leg and tries to escape with Sakura and Tokuro in pursuit. However, the lord catches Hanahiru first and kills her for stealing the Mononoke Leg. He then plans on killing Suzune as she is connected to Nurari, which sends Sakura in a rage. With both Sakura wanting to protect Suzune and Tokuro in vengence for Hanahiru, they battle the lord. Both manage to kill him, but not before sustaining mortal wounds, resulting in both their deaths but preventing Sakuraba from falling.
Timeline 4, Ending S
Before the group manages to destroys the research, Suzune takes Tokuro's piss jar and throws it at Hanahiru who was hiding. This distraction allows for Suzune to escape with the Mononoke leg. She takes it to the lord who she believes is the strongest to destory the leg and is willing to sacrifise herself to him. The lord does so but spares Suzune who he is impressed by her spirit. The group rushes in, thinking they are about to fight but are instead pardoned by the lord wanting to put this behind. They begin to leave but Tokuro prevents Sakura from leaving, filled with a frenzy and challenges her to a duel to the death. She obliges and they both battle each other, mortally wounding each other and damaging their weapons. Suzune, coming to the aid of her master, appears with new weapons and filling Sakura's spirit, allowing her to defeat Tokuro. Finally besting him, Sakura is the winner but miraculously both are recover with their bodies restored by Nurari. With both wishes being completed, Suzume is taken by Nurari as the timeline becomes changed, resulting in everyone surviving and the destruction of Sakuraba being prevented but Suzume being erased from everyone's memory.
Timeline 4, Ending SS
Although the future was saved, Sakura begins feeling the empty pressence of Suzune who she can not remember. However, after following the trails left in the suggestion box by Suzune, she is able to confront Nurari and manage to retake Suzune. Both Sakura and Suzune return home, where they continued to live as master and student with everyone. Years later, Suzune would become master of the Sakura and Tachibana styles become renowned. At the end of her life, her soul would be reunited with Nurari where they spend eternity with each other.
This timeline takes place years before the event of the Monsterous Horror Show game series and are interconnected.*