Hetappi Manga Kenkyujo R begins when a manga editor named Saito, exhausted by low pay and long hours, barges into the apartment of the manga artist Yusuke Murata and announces he wants to quit his job to become a professional manga creator. He insists that Murata teach him how to draw. The lazy but talented Murata, who is found working from inside a sleeping bag, reluctantly agrees to help his persistent former editor.

The story follows this unusual student-teacher relationship as Saito, a complete amateur who wears a Kamen Rider belt around his waist, learns the fundamentals of manga creation. The setting shifts between Muratas messy Tokyo apartment, where he works with his assistants, and various locations where they conduct interviews with successful Weekly Shonen Jump artists. Over the course of the narrative, Murata and Saito consult with several real manga creators who appear as characters. Mizuki Kawashita, known for romantic comedies, teaches Saito how to draw appealing female characters. Mitsutoshi Shimabukuro gives advice on character design and personality. In a notable arc, they attend a dinner with Yoshihiro Togashi, who discusses his approach to character emotions and expression, particularly how a characters feelings can be conveyed through their eyes. The series also follows two aspiring rookie manga artists, F-o and M-moto, who seek guidance on creating dynamic movement in sports manga.

Each chapter focuses on a specific technical topic, progressing from basic tools and pen practice to facial expressions, body proportions, creating movement, perspective, background art, and developing original characters. The narrative is framed as an educational manga about making manga, blending comedic interactions between the lazy artist and his eager former editor with practical, step-by-step drawing instruction. Alongside the main lessons, the book includes bonus pages covering how to submit manuscripts, the role of manga editors, and various Jump-sponsored manga awards. The story concludes with Saito gaining a foundational understanding of the craft, having moved from a disillusioned editor to someone who has experienced the challenges and techniques of professional manga creation firsthand.