Ten years ago there was a secret war fought by master mages with their servants in order to obtain the Holy Grail and the result was devastating to everyone. Today, the Holy Grail War is beginning again with new masters. One such master, Shirou, must now come to grips with the reality of the secret world of war mages and their summoned servants when he unknowingly summons his own servant, Saber, the one said to be the most powerful servant of them all. Perhaps Shirou will be the one to prevent the destruction that had marked the first war.

When he was little, high school student and amateur mechanic Shirou Emiya was adopted by a magus man. Now he wants nothing more than to follow in his stepfather's footsteps and become a hero of justice. Little does he know that a war is waging among some chosen magi, and that he is about to become its focal point...

The legend of the Grail continues! After suffering the deathly blow of the Berserker, Emiya wakes up with a mysteriously healed body. Determined to survive and defeat the Masters, Emiya sets out to unravel the mysteries of the Grail and how his past is somehow tied to his new powers.

The excitement continues as Emiya discovers the origin of the spell field only to be greeted by the Servant who controls it: Rider! As she attacks, though, Rider carelessly discloses a secret about the field to Emiya. Will Saber arrive in time to save Emiya from catastrophe? Meanwhile, our heroes discover something truly shocking as they scramble to find the cause of what ails the city of Shinto...

Shirou and Saber are in big trouble when they face off against Caster and her horde of undead soldiers. Will they be able to defeat Caster on their own or will Rin have to save Shirou again? And what will happen when the next Servant appears, and Saber chooses to defy Emiya's orders as her Master?

Shinji and Rider are up to no good again, and this time everyone is going to suffer. As Shiro wrestles with the dramatic changes in Shinji, he tries to change his old friend, believing that there's still good in him. Meanwhile, Shiro struggles to reconcile the growing complications in his relationship with Saber. What does it really mean to be Master and Servant, anyway?

Shiro activates his command mantra, summoning Saber to his side, while Rin and Archer attack Shinji and Rider, pushing them to the edge of defeat. But Saber blocks Archer's final blow - under Shiro's orders - promising to defend Shinji even at the cost of breaking their agreement with Rin. But can they convince Shinji to cease his immoral acts? And Rider questions Saber's loyalty to a Master who doesn’t even want to fight - just what are Saber's true reasons for obeying Shiro?