Kenji Noda is a central character in the film, a former naval weapons engineer for the Imperial Japanese Navy during World War II. Following the end of the war, he works as a crew member on a minesweeper, the Shinsei Maru, where his primary duty involves helping to locate and dispose of dangerous naval mines left behind from the conflict. His past as a developer of wartime weapons gives him a unique and highly technical understanding of machinery, explosives, and naval tactics, for which his fellow crew members have nicknamed him "Doc".

In terms of personality, Noda is portrayed as a highly compassionate, intelligent, and principled individual who stands in stark contrast to the callousness he witnessed during the war. He is a calming and reassuring presence, often offering comfort to the protagonist, Koichi Shikishima, who is deeply traumatized by his experiences and guilt over surviving the war. Noda demonstrates a profound respect for life, a value that directly shapes his actions and motivations. He becomes frustrated with the post-war Japanese government's inaction and disregard for civilian safety in the face of the Godzilla threat. His primary motivation is not revenge but a genuine desire to protect the people of Japan and to atone for a past regime that, as he puts it, "treated life far too cheaply" with tactics like poorly armored tanks and kamikaze attacks. He is determined that this new battle against Godzilla will be different; it will be a citizen-led effort where no lives are sacrificed, a fight "to live for the future" rather than one waged to the death.

Within the story, Noda serves as the strategic mastermind behind the plan to defeat Godzilla. When official channels fail, he orchestrates "Operation Wada Tsumi," a complex and ingenious civilian-led operation. His plan is unique, relying on using specialized equipment and scientific principles rather than brute force. It involves luring Godzilla into deep waters, rapidly sinking it with Freon gas to compress its body, and then using high-altitude balloons to violently force it back to the surface, hoping to kill it through the catastrophic effects of explosive decompression. His role is to devise this strategy, rally the crew of veterans and civilians, and lead the technical execution of the operation.

Key relationships are central to his character. He shares a strong bond with his fellow minesweeper crewmates, including the young and eager Shiro Mizushima and Captain Seiji Akitsu. His most significant relationship is with Koichi Shikishima, whom he consistently supports and comforts, helping Shikishima channel his wrath and desire for self-sacrifice into a more constructive and survivable mission. Noda’s development is less about personal change and more about the reaffirmation of his post-war values. He transforms from a man who once developed instruments of war into a leader who uses his knowledge to build a plan that prioritizes survival and collective action, directly rejecting the suicidal ideology of the past. His notable abilities are not physical or combative but intellectual and strategic, including his engineering expertise, his skill in devising complex tactical plans, and his empathetic leadership, which inspires a ragtag group of civilians to confront a monster that the formal military could not stop.