In Suisei no Gargantia, humanity has long since left the Earth behind and now lives under the Galactic Alliance of Humanity, a power devoted to exploration and survival in a war against the mysterious Hideauze. During one of those battles, 16-year-old lieutenant Ledo and his autonomous robot, Chamber, lose control and are cast far from the front lines, crash-landing on a planet that is now almost entirely covered by water.
There, Gargantia—a vast fleet of scavenger ships—finds Chamber and hauls the machine up from the sea, believing they have recovered something valuable. Ledo initially mistakes their actions for an attack and sneaks aboard the fleet, even taking a young messenger girl named Amy hostage before realizing that the people of Gargantia are nothing like the enemies he expected. Cut off from his comrades and unable to communicate with anyone from the Alliance, he must learn how this unfamiliar society works, adapt to a peaceful life at sea, and uncover the truth behind the ocean-covered world he has fallen into.