Lost in Blue follows two young teenagers, Keith and Skye, who struggle for survival on a deserted island.

The game's primary protagonist is Keith, who must lead Skye around the island by hand due to her poor eyesight.

In this mode, she can freely move about the island without assistance, although she is unable to climb as Keith can, severely limiting her range of travel.

Lost in Blue is not a linear game in its gameplay and its multiple endings provide a different story nearly every time one plays through it.

The next day, Keith crosses a nearby river and finds Skye asleep next to her raft, which is apparently undamaged.

After she wakes up, Keith and Skye meet for the first time and she tells him that she can't see very well because she has lost her glasses.

In the following days, Keith enters a routine of leaving the cave to explore the island and gather food and supplies, and Skye helps by preparing meals.

Eventually making his way to the other end of the temple, he discovers that there are in fact other people on the island, but his joy turns to caution when he overhears a conversation between the two men discussing their orders to kill intruders.