The Sky Temple on Dark Aether is the evil, twisted version of the Great Temple. It is where the Emperor Ing and Dark Samus await Samus at the end of Metroid Prime 2: Echoes. After Samus defeats the Emperor, Dark Aether will begin to die, and Samus must battle Dark Samus and escape before the dimension collapses.
The exterior of the Sky Temple bears little aesthetic resemblance to its counterpart on Aether, incorporating the Ing architectural mainstays of black stone and Ingworms. The Temple is also isolated from the ground in that it seems to float high up in the air, accessible only by teleporting (maps show that it floats higher than the Ing Hive Summit). Unlike its Aether counterpart, the Sky Temple has no elevators leading up to it.
- The Sky Temple's layout is upside down compared to that of the Great Temple.
- The Sky Temple is the smallest area in the game, containing three rooms. It is also the smallest final area in the Metroid Prime series, even smaller than the Impact Crater and Phaaze, the final areas of Metroid Prime and Metroid Prime 3: Corruption.
- Samus also has to defeat three guardians to get into the Sky Temple.
- The Light of Aether in this area is red but after defeating the Emperor Ing it becomes light yellow. This may suggest that the light was corrupted with dark energy when the Emperor Ing was alive.
- Although the energy here was supposed to be in the Energy Controller room, the Emperor Ing took it to its lair upon Samus' arrival. The room where the Emperor is battled is the Dark World alternative to where the first boss is battled in the game.
- Sky Temple is also the name of an arena in the Mortal Kombat series.
- Interestingly, there is a window on the ground near the teleporter to the Sky Temple Grounds, and if Samus looks through it, the ground cannot be seen. Instead, a black hole-like object can be seen.
- It is implied through room names, the presence of massive quantities of Phazon, and the Emperor Ing guarding it that the Sky Temple is in fact the Aether Leviathan, similar to the Impact Crater, and that the Ing enshrined it and worshiped their creator as a god.
- The Sky Temple is the only area in the Metroid Prime trilogy in which the Doors are raised above the ground, requiring Samus to jump in order to go through them.
- The Sky Temple shares its theme, Dark World Temple, with the Sky Temple Grounds.