"Heaven's Memo Pad" centers around Narumi Fujishima, a high school student who becomes entangled with a group of amateur detectives known as the NEET (Not in Education, Employment, or Training) Detective Agency. The agency operates out of a ramen shop and is led by Alice, a reclusive and enigmatic girl who rarely leaves her room filled with computer servers and stuffed animals. Alice is a genius hacker who uses her skills to gather information and solve cases, often relying on her team of misfits to carry out investigations.

The narrative unfolds through a series of episodic cases, each delving into the personal struggles and mysteries of the clients who seek the agency's help. These cases range from uncovering the truth behind a suicide to exposing corruption and solving disappearances. The stories often explore themes of loneliness, societal alienation, and the search for identity, reflecting the NEET lifestyle of the detectives themselves.

Narumi, initially a passive observer, gradually becomes more involved in the agency's work, forming a close bond with Alice and the other members. The team includes Hiro, a former gang member with a strong sense of justice; Ayaka, a former idol with a sharp tongue and a knack for undercover work; and Minoru, a middle-aged man with a mysterious past. Together, they navigate the darker corners of society, uncovering truths that are often painful but necessary.

As the series progresses, the episodic nature gives way to a more interconnected storyline, revealing deeper layers of the characters' pasts and the reasons behind their current circumstances. Alice's own backstory, in particular, becomes a focal point, shedding light on her isolation and the emotional scars she carries. The series balances its darker themes with moments of humor and camaraderie, creating a nuanced portrayal of its characters and their world.

The narrative is driven by a combination of detective work, emotional drama, and social commentary, making "Heaven's Memo Pad" a compelling exploration of human relationships and the complexities of modern life. The interplay between the characters and their evolving dynamics adds depth to the story, ensuring that each case feels personal and impactful.