Lost in Blue follows the relationship of the hero and the heroine who are trapped on a mysterious deserted island after a disastrous incident at sea. The young hero of the game awakens to find himself on a seemingly uninhabited island. After meeting another survivor, a 17-year old girl who has also drifted ashore, the two must work together to survive. While planning their escape, the two will learn survival skills, such as hunting, searching for food and building tools while uncovering the island's many mysteries.
In their quest to survive, players will utilize completely original gameplay concepts including many innovative mini-games throughout their adventures. Highlighting these innovations is the ability to close the lid of the DS while cooking food - resembling closing the lid to a pot - for a designated time period in order to ensure that the food is cooked to perfection. Close the lid too long and the food will be burned, while opening the lid too quickly will result in an undercooked dinner.
Also in their journey to survive, players must learn to share responsibilities between the main character and NPCs, as each character's actions will affect the dialogue and events in the game. In addition, after clearing the game as the hero, players can play as the heroine and gain a completely different gameplay experience. There are multiple game endings depending on the two players' lifestyle, relationship, dialogue and their manner of escape, all making for hours of adventurous gameplay.