In Thinkin' Things: Sky Island Mysteries, the player assumes the role of a detective paired with Joe Cluesteau of the Sky Isles who is tasked with solving various crimes that occur on the floating islands. There are 2125 inhabitants -- and thus suspects -- on the islands so it's important to gather clues. To do so, the player must participate in games related to basic logic and English phonetics. Aside from Clue Central, which is the detectives' home island, there are 3 other islands, each with a unique type of puzzle:

Rebus Isle: Solve rebus puzzles on this island, which are puzzles that involve forming words by adding and subtracting sounds based on various pictorial and animated clues given by the puzzle. For example, 'st' plus a picture of an earring leads to the word "steering". The game has a built-in spell checker/dictionary to help the player along with a hint system.

Airshow Isle: Plan and coordinate an air show.

Stadium Isle: Help Fripples (denizens of this particular island) find their seats in the stadium. There are particular rules that each Fripple must follow. For example, cheerleader Fripples only cheer if they sit in pairs.

After working through enough puzzles and collecting enough clues, the player is able to use the clues to narrow down the suspects in the database.