In a story set years in the past, Himura Yuu is a studious and diligent young man intent solely on maintaining his top academic position at Otowa Academy. One day, he meets a mysterious girl named Amamiya Yuuko, who, to his surprise, recognizes him. Memories of a distant childhood, memories rather left forgotten... meeting Yuuko again will force Yuu to confront the regrets and sorrows of their collective pasts and presents. In the present, Kuze Shuuichi may seem like a womanizer, but upon closer inspection, is a man who would rather be left alone. Hayama Mizuki, however, is not the type of girl who would let him be, especially after hearing the beautiful sounds of his violin performance. As Mizuki attempts to become closer to him, Kuze attempts to push her away—the tale of their budding relationship is darkened with undertones of an imminent tragedy.

On Christmas Eve, Hiro Hirono's bike is stolen by a girl chasing a thief who stole her purse. He gives chase and finds her unconscious and his bike ruined. The girl, Miyako Miyamura, soon awakes and the two begin to talk. After making sure she is okay, they end up spending Christmas Eve together. Later, Hiro finds out Miyako attends the same school as him and they begin to spend more and more time together, Miyako developing affections for Hiro. Kei Shindou—Hiro's childhood friend who has long held a crush on him—begins to become jealous and a love triangle follows. The series also tells the story of Renji Asou. One day, he meets Chihiro Shindou, the twin sister of Kei Shindou, at an abandoned train station. Even though she's very shy, they get along pretty well and begin meeting at the same spot everyday; however, Renji finds out that Chihiro was in a car accident years ago and as a consequence she suffers from a disability: her memory lasts only 13 hours. Nevertheless, after learning that Chihiro's dream is to write a novel, Renji finally decides to help her fulfill her dream while also trying to make her overcome the difficulties imposed by her condition.

The anime once again tells two stories.The first story takes place in the past. Himura Yuu meets a girl, Amamiya Yuuko who seems to know him, but he doesn't know her. However, he soon remembers that she was a girl whom he knew from long ago. Yuuko then tells him something which he never knew. He was her first love since then, and her first love has not ended yet. The second story takes place in the present, just after the events of Ef - A Tale of Memories.. Kuze Shuuichi meets the cousin of Asou Renji, Hayama Mizuki and spends a lot of time with her. Unknown to Mizuki, Kuze had contracted a fatal illness and has little time left to live. Kuze had decided to break all romantic ties, but things go bad when Mizuki tells him that she loves him.

The story revolves around the protagonist Hirono Hiro, a poor high school boy who draws shoujo manga for his living. One cold Christmas night after meeting a very strange woman in a church, who tells him that he's going to meet someone he has to meet, his bike gets stolen by another strange girl. He runs after her and finds her collapsed on the street. Her name is Miyamura Miyako and her bag got stolen by a man on a motorbike. Soon after, they start hanging out together, enjoying highschool life. Miyako falls for Hiro pretty quickly but naturally finds a rival in his childhood friend, Shindou Kei, who has been dictating Hiro's life since ever.