"Cells at Work! Kaze Shōkōgun" is a two-episode anime special that expands on the original "Cells at Work!" series, focusing on the human body's immune response to a common cold virus. The narrative centers on the body's cellular functions, personified as characters, as they combat the invasion of a rhinovirus. The story begins with the body's temperature regulation system failing, leading to a fever. This triggers a heightened state of alert among the immune cells, particularly the white blood cells, including the neutrophil AE3803 and the memory cell U-1196.

As the virus infiltrates the nasal cavity, the immune system mobilizes to defend against the infection. The narrative highlights the roles of various cells, such as macrophages, killer T cells, and helper T cells, as they coordinate their efforts to neutralize the threat. The virus, depicted as a cunning and adaptable antagonist, exploits weaknesses in the body's defenses, leading to symptoms like sneezing, coughing, and fatigue. The story emphasizes the importance of teamwork among the cells, as well as the body's ability to adapt and recover.

Key characters include AE3803, a diligent but inexperienced red blood cell, and U-1146, a skilled and protective neutrophil. Their interactions provide insight into the challenges of maintaining bodily health during an infection. The narrative also introduces new characters, such as the memory cell U-1196, who plays a crucial role in recalling past infections and guiding the immune response. The story concludes with the body overcoming the virus, showcasing the resilience and complexity of the immune system. Through its detailed portrayal of cellular processes, the series offers an educational yet engaging perspective on the human body's response to illness.