Once a prize-winning violin prodigy, Hajime gave up on music after his father, professional violinist Ryuuji Aono, was involved in a scandal that led the media to harass his family. Now living alone with his mother and entering his final year of middle school, Hajime struggles to find a new career path. However, the sound of his classmate Ritsuko Akine playing the violin inspires Hajime to dream of a musical career once more. With the help of Ritsuko, Hajime prepares to take the entrance exam for the prestigious Umimaku High School. But if he wishes to join Umimaku's orchestra, Hajime must overcome his past trauma and open himself up to new musical horizons.

As with both the Advanced Generation and Diamond & Pearl series before it, the Best Wishes! series begins with only Satoshi, headed off to the Isshu region, located far away from Kanto, Johto, Houen, and Sinnoh, with his Pikachu. After he meets up with the new trainer and rival Shooty and the region's Professor Araragi, he gains traveling companions in Iris, a girl from a town known for its Dragon Pokémon, and Dent, Pokémon Connoisseur and the Grass Pokémon specialist of the three Sanyou City Gym Leaders.

Yuu Koito has always been entranced with romantic shoujo manga and the lyrics of love songs. She patiently waits for the wings of love to sprout and send her heart aflutter on the day that she finally receives a confession. Yet, when her classmate from junior high declares his love for her during their graduation, she feels unexpectedly hollow. The realization hits her: she understands romance as a concept, but she is incapable of experiencing the feeling first-hand. Now, having enrolled in high school, Yuu, disconcerted and dispirited, is still ruminating over how to respond to her suitor. There, she happens upon the seemingly flawless student council president, Touko Nanami, maturely rejecting a confession of her own. Stirred by Touko's elegant manner, Yuu approaches her for advice, only to be bewildered when the president confesses to her! Yuu quickly finds herself in the palm of Touko's hand, and unknowingly sets herself on a path to find the emotion which has long eluded her.

Despite having seemingly quelled the war between their respective gangs, Raku Ichijou and Chitoge Kirisaki still carry on with their fake relationship. Eventually, as Chitoge's perception of Raku slowly changes, she even begins to see him as a little charming. Chitoge struggles to come to terms with her newfound feelings for Raku, as a new girl joins the slew of Raku's admirers and the competition among those vying for the yakuza heir's attention grows even fiercer. And amidst all this, Raku's search for his first love and the contents of the mysterious sealed locket continues in Nisekoi:, which picks up where the first season left off. [Written by MAL Rewrite]