Ms. Honda is a good friend of Dr. Tenma and Dr. Ushiyama. Tenma is very comfortable with her, calls her as "Honda-kun", and treats her like any of his male colleagues. The only time Tenma brings up Honda's gender is when he asks if a woman could bear to destroy a childlike robot.
Honda is a very serious and practical researcher. She is initially unsure if a robot like Astro would be dangerous, but soon warms up to him.
Honda partially oversees the development of the robot Tobio, and initially sees the robot as being overpowered and potentially dangerous. Honda and Ushiyama are the only witnesses to the robot Tobio's birth, and she helps maintain his location a secret. Honda also tries to provide guidance when Tobio begins to act strange.
When robot Tobio links with Atlas and wanders blindly into the city, Honda drives a robot disposal tank alongside Ushiyama and Tenma. The trio accidentally overload the tank when fighting over how to obtain Tobio, which sends them to the hospital. Honda survives the tank crash, and becomes comfortable with Tobio after witnessing him acting like a normal child.
After Dr. Tenma passes away, Ms. Honda continues working at the Ministry of Science. She can be seen working alongside Ochanomizu in various episodes. In "The Death Balloons", she provides damage assessment when Astro gets shot, and helps transfer Uran's mechanics into Astro.