Twenty-six-year-old Hiroto Suwa; his wife, Naho; and their old high school classmates—Takako Chino, Azusa Murasaka, and Saku Hagita—visit Mt. Koubou to view the cherry blossoms together. While watching the setting sun, they reminisce about Kakeru Naruse, their friend who died 10 years ago. Mourning for him, they decide to visit Kakeru's old home, where they learn the secret of his death from his grandmother. Filled with regret, Suwa and his friends decide to write letters to their 16-year-old past selves to set their hearts at rest. With the knowledge contained in the letter from his future self, 16-year-old Suwa has the chance to rewrite the future. What choices will he make? What will happen in this new future?

While taking a ferry to Fuuka Academy, new students Mai Tokiha and her sickly younger brother, Takumi, spot a girl adrift on the water. Shortly after bringing her aboard, the ferry comes under attack from an assailant who summons a mechanical monster. Despite still recovering from her injuries, Mikoto Minagi fends off the monster using a supernatural sword. Mai soon discovers that Mikoto is a fellow Fuuka Academy student with abilities called HiME (Highly-advanced Materializing Equipment). Female students with HiME are responsible for defending the academy and the local city from the monstrous Orphans. After several incidents at the school involving battles against these mysterious creatures, Mai learns that she is a HiME herself and is capable of summoning a Child, a mechanical creature capable of great utility and firepower. Now burdened with new responsibilities, Mai joins 12 other HiME as they safeguard the school from a threat they know little about all while protecting the ones closest to them.

Mikan Sakura is a normal 10-year-old girl. Optimistic, energetic, and overall a very sweet child, Mikan is the complete opposite of the aloof, intelligent, and somewhat cold-hearted, Hotaru Imai. Despite their glaring differences, the two girls have been best friends for a very long time. So when Hotaru suddenly transfers to Alice Academy, a prestigious school in the city, her best friend is devastated—especially when she hears of the horrible rumors regarding the academy's harsh treatment of students. Beset with worry, Mikan runs away to see her best friend! Upon her arrival, Mikan learns of Alices, individuals gifted with various supernatural abilities, and that the school is an institution built by the government to train and protect them. Discovering that she has her own unique powers, Mikan enrolls in the academy, and, after a lot of trouble, finally reunites with Hotaru. Gakuen Alice is a heartwarming comedy that follows Mikan and her friends' adventures in the academy, as well as their attempt to uncover the mysteries surrounding the problematic, fire-wielding student Natsume Hyuuga.

Naoya Mukai's crazy lifestyle of balancing his time between both of his girlfriends, Saki Saki and Nagisa Minase, is still as hectic as ever. Additionally, the blonde bombshell Rika Hoshizaki also has her sights on Naoya, complicating his already convoluted love life. As if things could not get more ridiculous, another girl inserts herself into the situation: Shino Kiryuu, who is determined to end Naoya's two-timing and ensure Saki's happiness. However, Shino harbors secret feelings for Naoya—a longing she believes she must forsake—yet simply cannot due to the deep attraction he inspires.