The game begins on a path in the forest of Lynlora near a village and moves to many settings, such as the gloomy Ogmire Archipelago and the drowned city and dungeon of the same name; Tikniki Swamp, which has a maze and a scene of riding shotgun on a giant turtle which you cannot steer; a fleet of balloons called the Sky Pirates' Camp; the Chinese-style land of Zen'Jai with lava rivers, three dragon lairs, of various elemental affinities, and the Warlord's Palace, which is like a maze; Stone Heath, with three combination-lock puzzles located in ancient stone circles; a multi-story dungeon called the Goblins' Lair; the Bone Lands, which surround a lava lake; a vampires' necropolis called the Gargoyle Cemetery, which leads to a Cathedral taken over by the enemy and a giant collapsed staircase in the Bell Tower; and a sky full of floating stones leading to Necroth's Realm and his Lair.

Skye suffers from a fear of drowning, so the game involves much jumping over water hazards, especially prevalent in Ogmire.

It has an arcade sequence of riding a fantasy beast through underground chambers without falling into lava pits or crashing into rock formations.

Her companion is a sarcastic gargoyle named Draak, who decided to rage against the game's villain, the evil wizard Necroth, and is voiced by Robb Pruitt.

A 300-page script, by lead writer and designer Andy Wolfendon, was written and submitted to Mars, which only asked to change a joke, utterances of "damn" and "remove all the snakes from the game."

[8] Executive Producer Dale DeSharone stated the game's concepts were inspired by the Skittles television commercials of the "Taste the Rainbow" campaign.

DeSharone led a team of over 50 people in Kyiv across two years, working on Darkened Skye simultaneously with M&M's The Lost Formulas.

[13] CNNMoney, however, called the use of Skittles in the game "the most blatant product placement since Chap Stick in those commercials for The Mothman Prophecies.

"[28] GameTrailers placed Darkened Skye as number two in their "Top 10 Shameless Licensed Games", behind Chase the Chuck Wagon for the Atari 2600.