Haruhiko's childhood friend Kirino had been eagerly awaiting the day that they'd once again be able to attend school together, but a misuse of Gift's mysterious power threatens to ruin the entrance ceremony.

Riko, Haruhiko's younger sister, returns home after several years. Things start to return to the way they once were, but what of Kirino's feelings?

Haruhiko is getting jealous that other guys are looking Riko's way, but why should he have these feelings if he's only her brother? Does Riko even see him that way?

On a hot summer day, Maki and the others invite Haruhiko and Riko to the beach. While there, he devises plans to get Haruhiko and Riko back on better terms.

Nami won't leave Rinka alone, so Rinka and Haruhiko pretend to be a couple in the hopes that she'll back off. Nami sees through their ruse and unleashes the terrible side of Gift's power.

Kirino is having misgivings about Haruhiko and Riko finally making up. As an unintended consequence of a witch's fake Gift, Haruhiko begins to see Riko as his late mother.

Haruhiko finds the witch responsible for the fake Gifts and discovers that she is, in fact, Chisa. In order to see Riko as herself again, Haruhiko is prepared to sacrifice some very important memories... and even the rainbow itself.

While on a school trip in Kyoto with Riko and the others in his class, Haruhiko finds himself unable to buy the love charm Kirino had requested, because his feelings lie elsewhere.

Upon returning from the trip, Haruhiko admits to Kirino that he can't return her feelings. She later accuses Riko of breaking an important childhood promise.

With Riko begging for forgiveness, an emotionally-broken Kirino has Riko give up her past with Haruhiko so she can stay with him from now on. Haruhiko is then forced to come to terms with his own severed past with Kirino.

Haruhiko struggles to come to terms with Gift's true power and how he can protect the one he loves, which leads him back to the very first Gift: a parting farewell from his dying mother.

With Riko's memories restored, Haruhiko sets about repairing his broken friendship with Kirino. Though Gift's power is gone, and the Eternal Rainbow along with it, Haruhiko and Riko vow to see the rainbow together again.

Kirino's family runs a Japanese inn, and her friends from school are helping out. Business has been slow due to a large hotel being opened up close by, and Haruhiko gets the idea to clean up the inn so that new customers may come in. During this time, Chisa, Rinka, and Yukari start acting strange whenever around Haruhiko.