The story focuses primarily on the heroine Rin Tohsaka. After her father's death, Rin enters the Holy Grail War only to honor the legacy of the prestigious House Tohsaka alongside her servant, the Archer. Soon, however, she discovers that Shirou Emiya, a boy from her elementary school days, has also been involved in the battles and saves him, unexpectedly, in a moment of fatal injury. Without delay, Rin sets out to put an end to the conspiracies surrounding the Holy Grail War alongside Shirou and his servant, Sabre. In this way, the story begins to explore the truth behind Shirou's powers and the nature of his inexorable desire to become a "hero".
The story of Clannad revolves around Tomoya Okazaki, a third year high school student who doesn't like his life. Tomoya's mother, Atsuko, died when Tomoya was young, leaving his father, Naoyuki, to look after him. After the accident, Tomoya's father became addicted to alcohol and gambling, and got into fights with his son. One day, Naoyuki, again arguing with his son, pushed Tomoya against the wall, severely dislocating his son's shoulder. Since then, Tomoya and his father have treated each other well, but in a distant way, as if they were strangers instead of family. This hurts Tomoya more than the old fights with his father, and the resentment of returning home leads Tomoya to constantly stay out all night. In addition, the shoulder injury prevented Tomoya from participating in his basketball club, and encouraged him to distance himself from his school and other activities. Thus began his life as a delinquent. Tomoya's best friend, Youhei Sunohara, who was expelled from the soccer club for a fight, is also a delinquent and often stays in his dormitory with Tomoya doing nothing. The story begins on Monday, April 14, 2003, at the start of the school year, when Tomoya happens to meet Nagisa Furukawa, a soft-spoken girl a year older than him, who is repeating the school year because she fell ill the previous year. Her goal is to join the drama club that she can't join due to her illness, but they discover that the drama club has been closed down after the remaining members have graduated. Since Tomoya has a lot of free time, he decides to help Nagisa restart the drama club. During this time, Tomoya makes friends with several other girls and gets to know them more deeply, helping them with their individual problems.