Commander Farragut's a man on a mission. That mission? Destroy the "giant narwhal." As Aronnax tells us, the American captain had one thing on his mind:
Either [he] would kill the narwhal or the narwhal would kill [him]. There could be no middle course. (1.4.1)
In the end, Farragut has to take that middle course. But his failure is not for lack of trying. He's simply outclassed by the Nautilus, unable to do anything to counter Nemo's mechanical monster.