There are slight variations in storyline depending on if one goes the Haruna (Real) or Takumi (Super) routes. Who is in which party tends to change, and there's a few occasions where they break up.
Starts off with Original Generation group located in Japan called Shin'i. They're made up of "Youkai", beings with special powers. They help out neutral and good supernatural creatures in Japan both by fighting evil beings, and fostering good relations between everyone else. They're a relatively small organization. They have ties to the supernatural community in Japan; so they roughly know the who's who of the Nasu Verse.
Starts off with a talking cat named Mike telling Takumi (The Big Guy with Green Hair) and Haruna (cheerful pink haired girl) that "Stagnation" is getting especially bad in Misaki City. "Stagnation" is The Corruption; magical energy gone bad due to something going very wrong. Misaki City is the city of Tsukihime and Melty Blood.
Even worse is "hallowed ground" where spirits come to life. "Hallowed" does not have the positive aspects of the western use of the word. (Think Terraria.) This happening quickly is unheard of, which is happening in Misaki City.
They arrive in Misaki and find that the Stagnation is so bad it has given birth to The Heartless.
Takumi goes to patrol the city, where he runs into Shiki Tohno; while Haruna goes to speak with the highest ranking Youkai in the supernatural community; Akiha Tohno. Akiha and Haruna knew each other in High School. Before she can do so, however, she meets Rin from Fate/stay night who is trying to find the Doll Mage, Touko Aozaki and had heard a rumour that she was in the city.
Takumi and Shiki Tohno are attacked by a wolf youkai familiar and Haruna and Rin are attacked by Nanaya Shiki; the Enemy Without of Shiki Tohno. Both encounters have their opponent deciding not to spend energy on them.
Meanwhile, Kohaku is in her secret lair under the Tohno Mansion, redesigning her Mecha-Hisui for the "Tohno Family Takeover Plan". To her surprise, the sword Excalibur teleports into her "Magic Kingdom" in a flash of light, and when she touches it, she gets bonded to the servant Saber. Never looking a gift minion in the mouth, Kohaku quickly accepts that a Magic Knight girl has chosen to call her Master. Her only manipulation is choosing to call her "Saber-chan." Interestingly, Saber is able to draw mana from Kohaku via an invisible Ley Line connecting them, usually something only a mage studying for many years can provide for a familiar.
At the same time, in the mansion above, Satsuki has broken into the mansion and kidnaps Hisui. Kohaku's Mecha-Hisui chases her, but are no match for a Dead Apostle; newbie or no; they have no magical resistance at this point. Saber and Kohaku try to stop her, but are held off by the appearance of Caster.
In addition, the 10th Death Apostle Ancestor, Nero Chaos (Nrvnsqr) has been resurrected. He is not an illusion dream of the Tatari, but claims to actually have returned Back from the Dead. And for some bizarre reason, Arcueid has decided to become a Magical Girl "Phantasmoon" using her Reality Warper powers. Her appearance causes Nero to back off; he's not prepared to challenge her yet.
Both groups (and Akiha) converge on a warehouse that is an obvious trap. Satsuki has been manipulated by Shiki Nanaya who somehow teleports her away when she is defeated; and Nero Chaos is actually Caster's Master. He leaves the group in Caster's care and she tells them that a new Grail War has started. She freezes them with a spell; but the spell is broken by the reappearance of Arcueid again. When "defeated", Archer appears and destroys Caster with his swords, and immediately leaves.
With Hisui rescued, everyone gets back to the Tohno Mansion to compare stories. Rin tells about the previous Grail War, and how she's looking for the mage Touko Aozaki because she needs her help. (This is because Shirou's doll body from the end of the Heaven's Feel plot of Fate/stay night is having some glitches, and they're looking for the Doll Master for help) she heard that she was in Misaki so she came to see if the Tohno Head knew where she was. Shiki is surprised that this mage has the same last name as his Sensei (they're sisters, but he doesn't know that) but nobody has heard anything. Everyone is given rooms at the Tohno Mansion for the time being. Rin doesn't want to impose on the Tohno's, so chooses to stay at a hotel instead.
Shiki reveals that he took Arcueid to see a Magical Girl movie the other day, and Arcueid got... inspired. Really, really, inspired. She decided to use her Reality Warper powers to become one. Church Militant Ciel sensed that there was a change in Arcueid, but is relieved yet aggrieved that "she hadn't fallen into darkness, but merely was doing something stupid."
Arcueid gets Shiki's cat familiar Len to act as her animal sidekick (all magical girls have one) and finds Satsuki elsewhere in the city. Satsuki is in a bad state; her blood lust is returning ten-fold. Arcueid comments that this is because Satsuki's Sire, Roa the Serpent of Akasha and the unnumbered Dead Apostle Ancestor, has been revived. Arc and Ren lose track of Satsuki, who runs away.
At this time, Rin's hotel is attacked by Nero Chaos. He is consuming the people who are staying here in order to charge up his power. This is the same hotel that Nero had done the same thing in Tsukihime. Whether Rin runs or fights, in the end Arcueid holds Nero off while telling Rin to find Shiki; he is the only person with a chance of killing Nero.
At the same time, the Tohno Mansion is under attack by the original SHIKI Tohno who has forced Rider to become his Servant. While Takumi's group is attacked by Roa who is working with Archer, Shiki Nanaya is Archer's Master, and has commanded him to help Roa. Archer is doing this willingly, Rider is not. Roa and Archer run away, and SHIKI is ignored (to his irritation) when Rin runs in and says that they have to stop Nero NOW.
Nero, when he was a human, was a mage. Hence his being able to be Caster's Master. And in addition to his vampiric self being resurrected, so was his magecraft. Despite Arcueid saying this is impossible; vampirism should have destroyed his mage core. Nevertheless using magic, Nero awakens his Chaos within (Before, Nero couldn't do this; his Reality Marble had to be hidden inside his body or the World would erase it as a paradox) and expands his Reality Marble to begin to consume everything. Shiki Tohno cannot get close to the sphere of magic to hit its Death Spot without getting sucked in. However, traditional magecraft has a weakness. A Legendary Sword can destroy any magic that it is older than; and Excalibur is older than both Nero and his magic. After instructing Kohaku how to use a Command Seal to focus the power of the Legend, Saber strikes Nero down. The combination of Excalibur, the World negating a collapsed Reality Marble, and the Command Seal annihilates him.
With that problem resolved, the crew focuses on the other Dead Apostle Ancestor(s) that has sprung up. Rin, upon discovering that SHIKI is the Master of Rider, phones home and discovers that SHIKI had attacked them and with the help of a white bird youkai threatened Sakura. Rider surrendered to him to prevent Sakura from getting hurt, and with the help of Rule Breaker (which Archer had Projected for him) bound her as his Servant. SHIKI breaks the truce, but Shirou and Sakura were saved by the arrival of Priestess Caren and Lancer. Since the events in Misaki City are clearly related to this, Rin advises them to come to Tohno Mansion for mutual protection.
After a number of skirmishes with SHIKI, Rider, Roa, Satsuki, and Archer, both groups corner Roa and SHIKI back to back over a bridge where the two who are one... fuse into the ninja, RoSHIaKI. He gets killed very quickly for this stupidity. Archer gets away and Rider is returned to Sakura. Shiki starts to talk some sense into Satsuki (by actually paying attention to her!) and she responds. Nanaya, irritated that Shiki didn't just kill Satsuki stabs Satsuki and she falls into the river. Shiki fights Nanaya, but Nanaya is too strong and stabs him as well. Shiki then falls into the river.
At the Tohno mansion, Akiha goes into shock since they weren't able to find Shiki. Kohaku manages to convince Saber to train her and Hisui with some combat techniques to try on Akiha protect Akiha. Saber doesn't really think they can learn anything too quickly in a day, but the promise of food convinces her to humor them and the two learn a Combination Attack. Akiha shows she is strong even while distracted, and opens a new technique with her Demon blood on some of The Heartless that had followed Len to the mansion.
Shiki has washed up on the riverbank, but is in the grip of a Nightmare. In his dream, Nanaya, Vermillion Akiha, and Feral Satsuki attack him. He cannot fight back, however, his body is discovered by his old friend Sion the half-vampire psychic alchemist mage. Sion uses her Etherlite to enter Shiki's dream and helps him survive his fear of his own bloodline. Shiki thanks Sion, and reveals that his opponent is himself in Real Life as well. Nanaya, the Assassin who is the Shiki who never was adopted by the Tohnos. This is something more than a mere Tatari Avatar, like they fought together in Melty Blood. This Nanaya is real; and Shiki has to somehow gain power in himself, learn how to train his strengths, and his Mystic Eyes of Death Perception. If only there was someone else who could train him who knew of the eyes. But that's impossible, two people couldn't both have them, could they? Shiki chooses not to go back to the Tohno mansion, or even tell them that he's alive, in order to gain power in his Self. After healing up by spending the night at Shiki's Muggle friend Arihiko's house, Sion uses her mind powers to make Arihiko think it's a dream.
Cut to someone completely different. Touko Aozaki and Shiki Ryougi of Kara no Kyoukai are in Misaki City due to a lucrative job that Touko has been hired to do. Ryougi is irritated that they've been away for long and Tohko teases her about calling Mikiya all the time. Tohko is aware of strange events occurring within the city, but has so far avoided all of them. However, they are confronted by White Len, who reveals that she is the familiar of Aoko Aozaki, Touko's sister, whom she hates. White Len gloats that Aoko tricked Touko into the job she's working on and then sics The Heartless on them just as Sion and Shiki Tohno walk in on the situation. Both Shiki's use their Mystic Eyes of Death Perception, which both parties recognize.
Touko finds out that not only has Aoko manipulated her into the situation, but she also has a person named Shiki with the Mystic Eyes of Death Perception. Touko assumes that it's to screw with her and decides to get involved. Sion uses her own mage knowledge of Equivalent Exchange of information to get Touko to agree to have Ryougi train Shiki in using the Mystic Eyes. After this, Shiki Tohno and Sion split ways; Tohno to train with Ryogi while Sion goes to find Satsuki, who she received a letter requesting help from (and the original reason she was in the city).
Sion finds Satsuki, who was discovered by Arcueid and Len again, and finds out that while Satsuki thought about writing a letter for help, she didn't send it. Enter White Len, who reveals that she was the one who sent the letter to get her involved. She also reveals that Sion's presence was required in order to resurrect the Tatari, who then appears. Tatari, the Cursed Nightmare that takes the form of people's anxieties and one of the Dead Apostle Ancestors. Since this is taking place in the ruins of the hotel that Nero killed in, the Tatari takes the form of Nero. Arcueid and Sion get Satsuki to join their group, and they defeat this Avatar of Tatari, while White Len escapes.
Meanwhile, Shiki Tohno is learning from Shiki Ryougi. Ryougi tells Shiki that what's holding him back is his fear of his self. The urge to kill is something to be mastered and partnered with, not pushed down or else it just comes up in inconvenient spots. By fusing his Mystic Eyes and accepting his Nanaya heritage, Shiki Tohno can become strong. In the end, it's Shiki Tohno who chooses to kill his enemies and not kill his friends. Shiki regains the power he had the first day he killed someone, and sliced them into 17 pieces. Arcueid. (She got better).
At the same time, Archer and his Master Nanaya attack the Tohno mansion. They are no match for Archer who beats him down mercilessly. Nanaya and True Assassin kidnap Sakura, while Archer stays behind to kill Shirou. Archer is about to kill Akiha, but Hisui shields her with her body and while Archer hesitates at this, Shirou reminds him that his feud is with him. Archer lets them go and beats Shirou down with his Unlimited Blade Works. Right before the coup de grāce, though, Shiki Tohno appears and drives Archer off with his new-found strength.
Another mass revelation time as everyone compares notes. A badly mangled Shirou recognizes Archer's Magic Phrase. It is his own. Archer is a Servant from the future, an alternate form of Shirou, who has come to kill him so that he wouldn't follow the same path he did. Shiki Tohno is scolded for not telling anyone where he's been, and Touko and Shiki Ryougi are introduced to everyone. Shirou promises Touko that if she helps them, he will repair Ryougi's prized katana, the Kuji, and Rin promises that she'll somehow contact Zeltrech and pay her in any amount of jewels she might want. Touko is unimpressed with promises, but the weirdness in the city is certainly something to watch and she repairs Shirou's body enough to fight.
Meanwhile, Sakura is talking to Archer, and finds out just who he is. A Shirou who lost all hope, whose dreams betrayed him. He tells Sakura that his heart died and his body continued; a walking hell. He is convinced that the Shirou who put his hopes and dreams in being only one person's hero, Sakura, is just as much a fool as he was, and that he will prove it. Then Zouken arrives to turn Sakura into the Dark Grail. Also, Shiki Nanaya seems to be having a breakdown. He isn't a killer of people, he's the killer within Shiki Tohno. All that matters is to kill Shiki Tohno or be killed by him, and they will become one.
Touko goes into preparations to start truly repairing Shirou's body. While Shirou is under the knife, in a dream he sees Archer's.... his Reality Marble. He rejects it, completely severing his link to Archer's future. At this point, however, Angra Mainyu attacks. All The Evil In The World, it is an infection within the Holy Grail. It's very presence causes Haruna to go berserk. She's... afraid of the Chaos, far more than the normal Stagnation or Nero's Chaos. She starts to get pulled into it, and Takumi powers his sword to the breaking point to free her. Fortunately at this moment, Shirou awakens, and using the Nine Lives attack destroys this part of Angra Mainyu.
However, Haruna is still infected with The Corruption, and she's left bedridden. It will eventually kill her. Takumi knows of someone that may help, but it will take 3 days for reinforcements from Shin'i to arrive with both a replacement for his sword and the ability to help Haruna.
The showdown between Shirou and Archer and Shiki Tohno and Shiki Nanaya occurs. Shirou defeats Archer and Shiki Tohno defeats Shiki Nanaya. Nanaya tries a surprise attack which Satsuki takes instead; this kills her unless certain actions were made previously in the game. (Essentially every time Satsuki was an opponent, Shiki had to fight her and talk to her.) Shiki finally kills Nanaya, telling him that his existence is over, that there is only one Shiki (well, not including Ryougi) and he will NEVER lose control. Archer accepts his defeat, and is about to disappear, but Rin makes him her Servant, with the threat that she'll make Shirou be his Master if he doesn't behave. Both are adamantly opposed to this.
The enemy never told Archer anything about their movements though, so he cannot share information. More power-ups, Shirou doesn't have the same spam ability of blades that Unlimited Blade Works gave him since he has rejected that Reality Marble, but he is still able to repair Ryougi's Kuji and provide Takumi with a temporary blade. Rin convinces him to try and project the Jeweled Sword of Zeltrech; however, he gets distracted and accidentally creates the Kaleidostick as well. An add-on to the Jeweled Sword, it takes over Rin's mind and turns her into a Magical Girl and she flies off to defeat evil. Arcueid isn't going to take this lying down, and decides to power-up by augmenting her outfit and breaking into the Throne of Heroes and stealing Caster's Moon Staff. Then Phantasmoon Eclipse and Magical Ruby have a Magical Girl-off where they defeat as many of The Heartless as they can. It's decided to be a draw. The good news, Rin now has the Jeweled Sword for a standard super attack. The bad news, if she sacrifices her dignity for power, she can become a Magical Girl.
Haruna's infection gets worse, and it's revealed that this is actually breaking down the seal on her power. She's partly clairvoyant and warns Takumi that a Black Giant and a White Girl are going to attack the Tohno Mansion. Rin instantly knows what this means: It's Ilya and Berserker. Ilya doesn't remember anything that happened in Heaven's Feel and has apparently reverted to her old self. Takumi tries to take on Berserker, but the Black Giant destroys his projected sword immediately. Fortunately, at this moment, Natsuki, the Meido of Shin'i in her...flying ...copter....thing and throws Takumi his strongest swords, the Futsu-no-Mitama: The first sword to ever kill a god. He drives Berserker back, something extremely that impresses Ilya. She declares Takumi to be Berserker's Rival now.
At the same time, Hisui accidentally breaks the magical protection that Touko put around Haruna to keep her from infecting anyone else. The piece of Angra Mainyu breaks off and is about to attack Hisui when Haruna distracts it and jumps out the window. Fortunately Ryougi is admiring her fixed Kuji and wandering the grounds (she's not really a people person) and catches her. A shadow image of Sakura commands the Angra Mainyu, but then Natsuki arrives and temporarily releases the seal on Haruna, giving her a power-up and curing her of The Corruption.
Natsuki tells the others that Shin'i's investigation has revealed that their enemy is trying to engage in the ancient Soul Suppression ritual. If enough souls are brought together by forcing power into the land, then any one enemy, no matter how strong, can be nullified. What exactly is the enemy's target is not known.
The gang heads out to find leads on Sakura's location and what they find is... Dark Sakura. But no, it isn't her. It's actually the Tatari, feeding on Rin and Shirou's fear. They defeat this Avatar and Shirou announces he's confident that Sakura is stronger now, the fact that the Angra Mainyu is only facing them and not eating townspeople means Sakura is resisting.
They split up, Takumi finds Ilya at Araya's Apartment complex.
Haruna finds Zouken and White Len along the river.
Both hint at the existence of Ilya's castle.
Archer, Rider, and Lancer infiltrate the back and find where Sakura is being kept. They find the true Sakura who despite being Dark, has cut off her mind so that she will not consciously destroy. They are interupted by Zouken, Angra Mainyu, and True Assassin. Archer orders the retreat, as they cannot stand against this, especially since Zouken is summoning Angra Mainyu's core.
A pincer assault is planned on Ilya's castle. Takumi and crew will charge through the front door. Takumi's crew first has to fight the Tatari, who has taken the form of Saber Alter; what Saber was under the power of Dark Sakura.
Takumi's crew find Ilya and Beserker. They beat them, but then get their asses royally handed to them by Gilgamesh, who kidnaps Ilya.
A second assault defeats Zouken and Assassin. Shirou manages to reach through to Sakura, and together they summon the power of their love to defeat the apparent last chunk of Angra Mainyu. However, as they leave with Sakura, Natsuki discovers that the souls of the beings they have defeated have been buried into the land; turning it into Hallowed Ground (Magical Land). Everyone is being manipulated.
Cut to some new people. The mage who never made it to the last Grail War, Bazett Fraga McRemitz, thinks the old Grail War is going on, and her servant Avenger is the origin of the Angra Mainyu. A man sacrificed by villagers who felt that by turning him into "All The Evil in the World" they could save themselves. The previous power was a manifestation of this. Bazett has acquired the power of the Grail, which means that her time resets every four days.
Sakura has decided to accept her Darkness, and wears darker clothing to show this. She can now control the darkness within and use it on enemies.
Bazett manages to kill Saber, but time resets.
This trick has been done before, by the Cat Familiar Len. White Len has chosen to use the time loop to launch an assault against the main characters, which eventually makes some of them aware of the time loop. Defeating her does not end the cycle and time resets again.
Bazett goes to the Einzbern castle, only to discover that, there is a new mistress named Irisviel. She explains that her presence is an anomaly. Since Avenger was killed earlier in that time loop by Berserker, she goes out and discovers that this isn't Fuyuki. She finds a Tatari Arcueid who cuts off her hand and feeds a drop of blood to Arcueid, which drives her crazy. The cast defeat Arcueid to save her. Time resets.
In addition, the nemesis of Shiki Ryougi, the monk mage Araya Souren is also aware of the dream. The barriers between awake, asleep, and time mean nothing to him. Curiously the only actual human who has been revived, he claims he was never killed. In some variations he is killed in the dream and in others he kills Ryougi and Shiki. Time resets.
Eventually Caren takes Lancer to meet Bazett. This results in both Lancer's and Bazett's death and Avenger reveals his power as the darkness of the Grail. This also gives them a clue, that the source of this is "where all of Misaki can be seen", and this is the only place where Avenger can be defeated. Time resets.
Shirou figures out that the only place that "sees" all of Misaki is the Moon. There is an invisible staircase at the top tallest building that leads to the moon. But as they climb, they are interrupted by the Tatari, who takes the form of Saber Alter again.
Avenger possesses Shirou and they defeat Bazett, who just didn't want to die. (It was a dream created by Avenger as part of Bazett's wish). She had lost her arm with Lancer's Command Seals to Kotomine before. She's about to accept the termination of the time displacement, when Irisviel von Einzbern and Kiritsugu Emiya (Ilya's mother and Shirou's adopted father/Ilya's biological father) appears. He separates Avenger from Shirou and kills him. They want the loop to continue. Time resets.
The cast challenge the Moon again, and find out that Irisviel and Kiritsugu were given a chance by the Grail to keep their wish going as well. As long as time resets, Ilya (who will die a year after the Grail is summoned even if she isn't killed) will have time to live her life. They are defeated. Avenger and Bazett part ways, and Bazett chooses to join the group. Since she had been healed by Caren and wasn't in danger of dying.
The crowd in Tohno Mansion is getting pretty packed and they eat a lot of food, so Saber and Kohaku go out to buy some food. Saber and Kohaku begin to share their past traumatic experiences with each other, and Kohaku promises Saber that she'll do anything she can to help her. She'll tell Saber all of her secrets, as long as Saber tells her hers.
And this is tragically cut down by the appearance of Gilgamesh, who strikes at Saber with Ea, the Star That Cleaves the Heavens. Kohaku takes the hit instead which takes her down in a ripped up heap. Saber is in tears; she couldn't save Kohaku. Kohaku tells her that she wasn't thinking; that she just was doing what Saber would have done.
Back at the Tohno mansion, Touko tells everyone that Kohaku's chances are grim. It could take years for her to recover and even then her body functions would be shattered. Saber goes into Kohaku's room and apologizes to her. Kohaku wakes up, and tells her that is she would have been sad and lonely if Saber had left her. When Saber tells her it's her job to defend her, Kohaku simply states that it is pointless to argue with Saber about why she would save her if Saber will not listen, and goes back to sleep.
Touko is shocked. No human being should be conscious the day after that kind of damage. Apparently Kohaku is somehow healing magically. The subject goes to how Shirou was able to heal quickly when Saber was his Servant. (In Heaven's Feel, they never find out about Avalon). It seems too strange a coincidence, but somehow Kohaku is tied to Avalon. Not nearly the level that Shirou was; but it is there a little. Hisui then says that Kohaku had found a sheath "somewhere" and that she kept it underground. The cast goes to retrieve it, and by Saber being in close proximity to Kohaku, she begins to heal and recover fully. Saber tells her about her past and Kohaku reveals that she already knew; that she had been seeing Saber's past and dreams when she slept. She tells Saber that neither of their wishes can be solved with the Grail but that it would be a good thing for Saber to stay with them if possible after this War. She could learn a lot about leadership from Akiha, for example, and how leadership only works when people cooperate with the leader. (And... she would be able to stay with Kohaku. But Kohaku is smart enough not to play emotion over Saber's sense of honor.)
It is at this point that if Kohaku and Hisui have killed enough enemies in the Real Route, Mecha-Hisui becomes playable.
Time for the end game. The gang takes Gilgamesh out by having Archer counter his Gates of Babylon, Saber counter his Ea, and Arcueid and Bazette wail on him. However, it turns out that Araya is really Gilgamesh's master this time around, and he sacrifices Gilgamesh to open the Path to the Akashic Record. The cast finds Ilya, but leaves her alone as surely she won't work with the people who kidnapped her. (This is not true though).
The Grail opens, and a tearing is sensed throughout Misaki. Araya and the true form of the Tatari attack the cast. Araya's power amplifies that of the Tatari, but his barrier also fully pulls it into the physical world. They are both defeated.
The final battle occurs and the Mastermind behind these events is revealed to be Kuu; an ancestor of Haruna's. Kuu has foreseen a devil born of the malice of mankind emerging in Misaki, and unless stopped, will kill countless millions. By cobbling together the pieces of the Holy Grail and "glueing" them together with the power of the Tatari, she has resurrected the old villains and used their life force to feed into the land and make it viable for the Soul Suppresion Ceremony. The ritual requires an enormous amount of people to die, so she'll then unleash the Tatari/Grail and kill most of Misaki City. Then she'll direct herself and the Soul Suppression ritual through the hole left from the incomplete Grail ritual to the Akasha where The Devil is waiting and nullify herself and the Devil. As a trump card, the Earth itself accepts this plan and brainwashes Arcueid into fighting against the party.
By defeating Kuu and Arcueid, the party convinces the Earth that they have a better chance at defeating The Devil. So they enter the path into the Akasha.
They defeat the horde of pieces of the Devil's soul, but it's not enough. However, Ilya, in her Grail form, draws forth the Devil's soul into one target for the heroes to face and it is destroyed. If enough Battle Masteries have occurred, Aoko Aozaki will help out.
Should enough Battle Masteries occur, then a small "epilogue" fight will occur where Touko faces Aoko who has a broken piece of the grail as her "payment" from Kuu. They win, but it's clear Aoko was screwing with them and lets Sakura have the grail piece before being teleported away by Kuu.
Sakura, using her mana and the grail piece, makes it possible so that Saber can stay with Kohaku for the time being. Everyone starts going their separate ways. Bazette decides to travel around the world with Sion to help with her vampire research, a physical mage would greatly help in capturing vampire test subjects. Saber stays with the Tohnos and Akiha enjoys her new power as the master of Saber's Master by informing Saber that they cannot begin meals unless everyone is at the table; including Shiki who has disappeared again. The words barely leave her mouth when King Arthur practically teleports away to drag Shiki back to dinner so that they can eat. The source of much Hilarity Ensues to come.
With all Masteries Completed, the Tohno Family Master Plan begins. Successfully stopping it unlocks Saber Lily and Magical Amber in New Game+. In addition, beating the game once gains an item called the "Abnormal Agonist" which increases multiple stats.