The series consists of three timelines:
The first one takes place before the accident, which is mostly contained in the first two episodes and covers the development of the relationship among Haruka, Mitsuki, Shinji, and Takayuki in their third year of high school. In Japan high school comprises grades 10 to 12 with students entering high school at age 15 or 16. Akane is also introduced. However, later episodes flash back prior to the beginning of this timeline and also depict photographs of events that happen in this timeline but are not shown; for example the photograph of Mitsuki, Akane, Haruka, and Takayuki at the pool. This timeline ends with all the friends at the hospital with a shot of Takayuki collapsed on the floor and Mitsuki wearing the ring that Takayuki bought on her left ring finger, much like an engagement ring. Unlike the US, the left ring finger is not reserved for engagement, wedding, chastity rings, or less common promise rings in Japan.
The second timeline takes place one year after the accident. As a prelude to this, Takayuki arrives as the ambulance takes Haruka away from the scene and he witnesses the still fresh pool of blood next to Haruka's bloodied hair ribbons. This traumatic experience causes Takayuki's PTSD, which is portrayed in episode 5 of the series. This has affected him more than Mitsuki and Akane. Takayuki and Mitsuki both experience flashbacks, emotional detachment or numbing of feelings (emotional self-mortification or dissociation), insomnia, avoidance of reminders and extreme distress when exposed to the reminders ("triggers"), loss of appetite (Takayuki), feelings of misplaced guilt, memory loss (may appear as a difficulty of paying attention as with Mitsuki), excessive startle responses (animated as visual changes in the pupils of the eyes), clinical depression, and anxiety three years after Haruka's accident. Akane suffers from hyper-vigilance, misplaced guilt, and irritability. Haruka herself is left in a coma. At the end of this timeline, Haruka's parents ban Takayuki from seeing Haruka after he tries to remove her from hospital while comatose. Mitsuki offers herself sexually to Takayuki while he is at his emotional low point following the incident. Akane discovers an undressed Mitsuki on Takayuki's futon the next day.
The third timeline takes place three years after the accident. Takayuki is now working part-time at a restaurant called "Sky temple", along with the comic relief characters Ayu and Mayu. Mitsuki and Takayuki have agreed to live together but have difficulties finding a new apartment. Eventually, Haruka awakens from her coma, oblivious of what has happened during the last three years. In addition, she is diagnosed with anterograde amnesia.
After having been awake for a month, Haruka still thinks it is three years ago. Akane contacts Takayuki to inform him that Haruka has awakened. The doctor warns Takayuki and Mitsuki that her condition is very fragile and informs them of the condition of her memory before they enter the room. She tells them not to let her know that three years have passed because she feels the shock would damage her psyche, possibly destroying her will to recover, and trigger a relapse. This does happen when Akane tells Haruka that three years have passed, Takayuki has been dating Mitsuki, and that everyone has been working to deceive Haruka. She then falls into another coma, although she wakes a few days later.
Haruka improves after seeing Takayuki. The only thing she can remember since the accident is Takayuki's visit. Takayuki is conflicted with his feelings of guilt and responsibility and must choose between Mitsuki and Haruka. The bulk of the rest of the story focuses on the suffering of the characters because of this predicament. Takayuki chooses Mitsuki after saying farewell to Haruka.
The plot consists of a blend of multiple game storylines, mostly the Mitsuki storyline with a bit of Haruka's storyline mixed with elements from the Akane storyline. The general fate of Amakawa is also disclosed through one scene between Fumio and Takayuki and a line by Fumio at the end of the final episode indicating she died. Manami is limited to one line at the very end and several dialogueless cameos. Materials not included in the game due to its perspective being in first person, such as depictions of Mitsuki having sex with Shinji (in certain routes) and Haruka telling Mitsuki that she has a crush on Takayuki while walking home, are also included.