The Commanding Admiral of the First Escort Fleet, he was in charge of delivering the fleet's vector-based attack craft for use against the conspirators at the island stronghold, to recover information about the Diclonius virus being unleashed by its insane leader. He was a career officer, told little about the threat and its nature, other than that it was dire, and that he was among millions infected with the Diclonius virus. He was bothered by the presence of the arrogant intelligence operatives aboard his command, who killed one of his men and ordered the Commander be bound and gagged at one point. The JSDF lost the First Escort Fleet and much of its air support en route to and from the island. After freeing himself and overpowering the second operative, the Commander met his fate along with the rest of his crew via a tidal wave created by Lucy's anger when Kouta was accidentally shot and wounded by Kurama.
The Commander's presence and storyline show how regular military officers were eventually dragged into the Diclonius conflict, and treated as only slightly less disposable than contract security or special forces. In the former case, it was to serve the agenda of Chief Kakuzawa. In this case, it was in the name of keeping quiet the Japanese government's prior involvement in supporting the Chief. The irritation of the Fleet Commander towards the vague and deceptive nature of his charges was probably not the last felt by a Japanese military officer in this conflict.
Do the military personnel in the series evoke your sympathy?