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.

Satoshi, Iris & Dent continue their travels through the Isshu region. After successfully winning his 8th Gym Badge against Homika in Tachiwaki City, Shirona invites everyone to stay at her villa in East Isshu, where old friend Hikari is also staying, and participate in the Pokemon World Tournament Junior Cup before Satoshi participates in the Unova League. Team Rocket, meanwhile, initiate their final plan for the Isshu region-what is their purpose in their desire for the legendary Pokémon Meloetta?

One day after school, Asahi Kuromine stumbles upon the truth that Youko Shiragami, the girl he has a crush on, is actually a vampire. According to her father's rules, Youko must now quit school in order to keep her family safe. However, Asahi does not want her to go and promises that he will keep her true nature secret. Unfortunately, this turns out to be easier said than done, as Asahi is a man who is easy to read and is unable to keep any secrets to himself. And this is the only the beginning of his troubles—more supernatural beings enter his life, and he is forced to protect all of their identities or face the consequences. Jitsu wa Watashi wa follows Asahi as he deals with his new friends and the unique challenges they bring, struggles to keep his mouth shut, and desperately tries to win Youko's heart in the process. [Written by MAL Rewrite]

In the 16th century, the city of Florence booms with cultural and creative revival in celebration of the Renaissance. Arte, a delightful young lady from an aristocratic family, dreams of being an artist and contributing to the renewal of civilization. However, with her father's death, she ends up losing the only person who believed in her passion for art. Now she is expected to marry a nobleman and live as a refined housewife without disgracing her family name. Reluctant to accept her fate, the headstrong Arte steps into the streets in search of a master artisan to take her on as an apprentice. In her quest for a mentor, Arte has to face harsh reality when she is completely shunned for being a female artist. No one believes that women are capable of fine craftsmanship, and therefore none are willing to accept her. Luckily, a renowned artisan by the name of Leo is persuaded to take her as his disciple since he has none anyway. And thus, Arte's new life begins, far from the comfort of her noble upbringing. As an apprentice, she must earn her keep while tackling various challenges along the difficult path to becoming a full-fledged, master artisan. [Written by MAL Rewrite]