The start of high school life. To the girls, that also meant the start of their love lives. For brand new first year student, Takahashi Nanami (Nana for short), it was no different... She happens to end up in the same class as the incredibly popular Yano Motoharu, who rumors say that two thirds of all the girls are guaranteed to fall in love with. But will that hold true for Nana, who says that if she had to choose between like or dislike, she'd say she dislikes him!?

In 2005 Bokura ga Ita won the Shogakukan Manga Award for shoujo. Nanami Takahashi, a teenage girl in her first year of high school, hopes to make new friends quickly. The center of attention at her school is Motoharu Yano, a very popular boy, whom Nanami dislikes at the beginning, due to his apparent superficiality. However, she soon falls in love with him, but Yano is still affected by the loss of his girlfriend, Nana Yamamoto. Nana was killed in a car crash a year before the beginning of the story. Because she was with her ex-boyfriend at the time of her death, Yano suspects she was cheating on him. Due to this, he is unable to trust people or to talk about his relationship with her; instead, he chooses to pretend he does not care very much about the situation.

Nanami confesses her love to Yano, but is rejected when he is unable to tell her if he loves her back. Despite that, she is still willing to support him and reassures him she will always be by his side. Soon, Yano realizes he has fallen in love with her as well, so they start going out. However, Yano's secrets (including the fact that he slept with Nana's little sister, Yuri, after the accident and his unwillingness to talk about his feelings for his dead girlfriend) make Nanami unsure to the point that she decides to end the relationship, believing she is unable to make him happy. The story becomes even more complicated when Masafumi Takeuchi, Yano's best friend, also falls in love with Nanami and becomes Yano's rival.

Due to these circumstances, Nanami is confused over whom she should choose, but she soon realizes that Yano is the one she genuinely loves. She agrees to start going out with him again, on the condition that she can find out more about the relationship between Nana and Yano and his true feelings about what had happened. Their romance takes an unexpected turn when Yano finds out that his mother, Yoko, wants to move to Tokyo. Upon hearing this, Nanami tells him to make a decision without taking her into consideration. The anime ends with Yano's departure; however, the two of them decide to continue their relationship.

The manga picks up four years later. It is revealed that Yano and Nanami kept in touch for about six months, then he stopped contacting her and disappeared without a trace. Tired of waiting, hurt and confused, Nanami starts a relationship with Takeuchi. Even so, she is still in love with Yano and unable to forget about their common past. She befriends a co-worker named Akiko Sengenji, who is revealed to be one of Yano's classmates from the Tokyo high school he transferred to. In a series of flashbacks it is shown that Yano was forced to work part-time when his mother was diagnosed with cancer, but kept everything hidden from Nanami, not wanting to worry her. Following an unexpected visit from Michiko, her former friend and wife of Yano's father, Yoko became increasingly paranoid, fearing he would leave her. When Yano announced his decision to go and visit Nanami, she accused him of being insensitive. After a short, but violent fight, Yoko hung herself; as in Nana's case, Yano blamed himself for her death and therefore decided to sever all the ties with his past.

Sengenji is also in love with Yano, but, despite this, she sees Nanami as a friend, not as a rival. She is the one who reveals Yano's whereabouts to Nanami (including the fact that he adopted his father's name, Nagakura) and later the fact that he lives with Yuri Yamamoto. As a result, Nanami rejects Takeuchi when he proposes to her, feeling that it wouldn't be fair to marry him. Upon meeting Nanami for the first time in more than five years, Yano claims he is in love with another woman. However, when he and Nanami meet again, she tells him that she knows about the relationship between him and Yuri. He then admits that he only stays with Yuri because her mother is dying and he feels he can't leave her alone. He also tells Nanami about his mother's suicide, and also about his panic attacks. During this meeting, it is hinted that he's still in love with her.

Meanwhile, Takeuchi decides to continue his relationship with Nanami, but only as friends. He tells her that she will eventually reach Yano and asks her to wait for him. He also starts to push Yano to admit his own feelings for Nanami and points out that no matter how strong she seems, she is unable to deal with the situation by herself. Nanami and Yano have an unexpected meeting, during which Yano finally confesses he wanted her to hold him back instead of letting him leave with his mother. Shortly after, Yuri's mother dies, which prompts Yuri to end her relationship with Yano. She reveals to him that her sister Nana never cheated on him and that she only wanted to have a proper break-up with her ex-boyfriend at the time of the accident.

Yano decides to start over with Nanami and tries to contact her on the telephone. He fails several times due to her busy schedule, but eventually reaches her. During their conversation, Nanami is involved in an accident and brought to the hospital unconscious. Terrified by the possibility of losing her, Yano rushes to her side - as a result, the two of them are reunited. The finale of the manga shows Yano proposing to Nanami and then visiting Nana's grave site with her.