Daddy Long Legs is based on the novel of the same name by Jean Webster. It chronicles the adventures of Judy Abbott, an orphan in New York. During a meeting for the superintendent, with other important and rich people in attendance, a scholarship is offered to Judy by a mysterious benefactor. Catching only a glimpse of his tall shadow as he leaves, Judy calls him "Daddy Long Legs" and writes him letters every month as per his request. While studying at the Lincoln Memorial school, she makes many friends and learns about a world she never knew about before. (Source: ANN)

While the young Angelique lives out her days peacefully in her school, attacks from the monstrous Thanatos has been increasing everywhere else. Two Purifiers show up one day, men with the power to exterminate the Thanatos. One of them, Nyx, attempts to convince Angelique to join them in their work, as she has the power to be the only female Purifier. As Angelique hesitates, a Thanatos shows up in their school. Nyx and the other Purifier, Rayne, fight a losing battle. With her classmates falling prey to the Thanatos, and the Purifiers beaten to submission, Angelique's desire to save everyone awakens. She became the only female Purifier in their land of Arcadia, the one known as the "Queen's Egg".

Continuing where the first season left off, the sudden increase of Thanatos with the disappearance of the Aube Hunters has now left Arcadia in ruin. Desperation reigns high as the Religious Organization fights to battle the Thanatos. Six months had already past since Hidamari mansion burned to ashes, the Aube Hunters, once hailed as heroes, is now blamed for the appearance of Thanatos. Nevertheless, hope still exists for the reappearance of the Queen's Egg one day, who will become the savior of Arcadia. Unknown to many however, the Aube Hunters have actually been silently waiting for the awakening of Angelique, who has been asleep the entire time.

Nana Komatsu is a helpless, naïve 20-year-old who easily falls in love and becomes dependent and clingy to those around her. Even though she nurses ambitious dreams of removing herself from her provincial roots and finding her true calling, she ends up traveling to Tokyo with the humble reason of chasing her current boyfriend Shouji Endo. Nana Osaki, on the other hand, is a proud, enigmatic punk rock vocalist from a similarly rural background, who nurtures the desire to become a professional singer. Putting her career with a fairly popular band (and her passionate romance with one of its former members) firmly behind her, she boards the same train to Tokyo as Nana Komatsu. Through a fateful encounter in their journey toward the metropolis, the young women with the same given name are brought together, sparking a chain of events which eventually result in them sharing an apartment. As their friendship deepens, the two attempt to support each other through thick and thin, their deeply intertwined lives filled with romance, music, challenges, and heartbreaks that will ultimately test their seemingly unbreakable bond. [Written by MAL Rewrite]