Kiyotaka Ayanokouji enrolls at the prestigious Tokyo Koudo Ikusei Academy, but is assigned to Class 1-D, where students with behavioral problems are housed. The school awards points equivalent to 100,000 yen per month and allows unusual freedom in classes, masking a more complex system.

Alcohol, smoking, and stress—in the body subjected to these irritants, the cells responsible for maintaining life seem to fight a war that never ends. Due to a severe shortage of workers, Red Blood Cell AA2153 has to quickly learn to deliver oxygen and collect carbon dioxide, even in dangerous conditions. Meanwhile, White Blood Cell U-1196 has to do her part by dealing with germs and viruses during life-threatening situations. In the midst of these crises, they have to work together to keep the body healthy, despite not knowing if their sacrifices will be worthwhile. Cells at Work! Code Black takes a different approach by showing the grittier side of the jobs our cells perform.