The large machine parts found in the Sanctuary Temple foreshadow the appearance of a fully assembled Quadraxis, the area boss found in the same area on Dark Aether.
Each sub-guardian in the game is a power-up enhanced version of an enemy already encountered in the game. The Bomb Guardian is a large Sandigger; the Jump and Boost Guardians are enhanced Hunter Ings; Grapple Guardian - enhanced Grenchler; Spider Guardian - enhanced Pill Bug; Power Bomb Guardian - enhanced Sporb. The same goes for the big area guardians: Amorbis is a large Sandigger, the Adult Chykka is a large War Wasp, Quadraxis is an enlarged Quad machine, and the mutated Emperor Ing is essential a grotesque Hunter Ing.
This is the only game in the series to feature beam weapons with limited ammo (the Dark, Light and Annihilator beams).
The area boss in Dark Aegon Wastes, Amorbis, consists of three giant worms that jump in and out of the sand. Some fans regard this as an homage to The Legend of Zelda: A Link to the Past (1991), a game that also featured a normal 'Light World' and a corresponding evil 'Dark World'. In Link to the Past, the second dungeon has bosses called Lanmolas, which are also three worms jumping in and out from the sand.