Thanks to the efforts of Lieutenant Yoji Itami (now Lieutenant First Class) of the Japan Ground Self-Defense Force, the once-closed "GATE" has safely reopened. The Japanese government, determined to maintain exclusive control over the "GATE", continues mobilizing the Self-Defense Forces for political and topographical surveys to build a peaceful relationship with the inhabitants of the Special Region. Captain First Class Edajima Goro of the Japan Maritime Self-Defense Force (JMSDF) and his subordinate, Petty Officer Second Class Tokushima Hajime, a skilled former chef, were conducting such diplomatic and investigative missions, traveling across the various nations of the Special Region.

However, one day, their assignment suddenly escalates when they're tasked with a special mission to rescue an American journalist kidnapped on an island in the Special Region's Blue Sea.

Immediately boarding the JMSDF Oyashio-class submarine Kitashio, they set sail into the ocean of another world, discovering the area around the Blue Sea engulfed in turmoil, with archipelago nations and pirates battling fiercely for dominance.

(Source: GATE 2: Tides of Conflict Site)