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Sky Troops takes place high in the sky, across the now-flying ruins of Glyphic Canyon, where the Black Arms are in the middle of a large-scale clash with the Eggman Fleet. Many of the areas are separated by floating platforms, and Cell Cannons can be found throughout.
Dr. Eggman laments about how the conflict between the Black Arms, Shadow the Hedgehog, and G.U.N. is destroying key locations he plans to capture, before sending his fleet to counter the alien threat. The game then sees Black Doom reveal to Shadow that the ruins in Glyphic Canyon were a massive flying fortress that he brought to Earth thousands of years prior. Black Doom then tasks Shadow with taking out the Eggman Fleet using Cell Cannons, while Dr. Eggman tells Shadow to destroy the temple jewels keeping the ruins in the air. The neutral path sees Shadow headed for the Goal Ring at the end of the stage, like most other stages in the game.
Beyond the second checkpoint after the jumping section, a key can be found directly to the left of the doorway leading to the ramp with the crumbling pillars.
In the temple area with the second battleship, a key can be found behind a pillar directly to the left of the staircase.
From the fourth checkpoint, the player should take the lower path; a key can be found a wooden platform off to the right.
Further ahead in the stage from the third key, the player must Light Speed Dash along the ring trail in front of the Jump Panel in order to reach the platform with the Cell Cannon; the key is directly to the right of it.
During the Black Volt flying section, the player must jump down from it and travel to the end of the cave; a key can be found on a platform floating just below the ledge.
The secret door can be found directly ahead of the sixth checkpoint, and a Black Volt and a worm launcher can be found behind it. Shadow can tame it to ride it through the rest of the stage, and the worm launcher makes it easier to collect Item Boxes along the way.
The first Eggman Ship is located just after the first Checkpoint. This is an easy target, and should help you get acquired with how to use the Cell Cannon.
Another easy to find ship, this one is in your way, so don't worry about missing it. When you are firing at it, aim a little ahead of Where it's going to be, because it is moving to the left. The turrets are a little hidden as well, making it a more difficult shot.
After the fourth Checkpoint, take the lower path, and you will find Eggman's third battleship. This one is the easiest for you to get hit.
After defeating the third battleship, you will come up to a line of rings above a speed boost Panel. Use the Light Dash to reach the fourth Cell Cannon and the fourth battleship.
This is the flagship, and it is equipped with eight turrets: three on each side and two in the middle. Lucky for you there are two Cell Cannons at your disposal in case you lose one. Take out the center turrets first, otherwise the battle will be much more difficult. If you obtained all five keys, you can use a Black Volt to take it down easier.
The first one is located behind the door after Checkpoint 2 Watch out for the Black Arms guarding the jewel. These Soldiers have a weapon that fires a ring laser that has a wide range, so watch out!
The second Temple is located after Checkpoint 3. After you break the jewel, two enemies must be defeated in order to open the door. To defeat the Black Arms Soldier with the shield, you must use the Homing Attack.
This jewel is on the bottom level guarded by two large Black Arms. Defeat the Black Arms and the Jewel is yours.
Right after the fifth checkpoint, you will enter another room. Defeat the enemies in this room, and continue to the end of the stage where the final jewel is located.
The last jewel is located at the end of the stage near Eggman's Flagship. You can get to it easily by going to one of the Cell Cannons, and jumping on the rising platform to raise you up to the last jewel.
Also, just like the dark mission, the Shadow Rifle is extremely helpful.
This zone is apparently an ancient weapon that was dormant until Black Doom's Arrival in Shadow the Hedgehog.
This is the only level in the game where Dr. Eggman, who is usually the guide for Dark Missions, appears as a guide for a Hero Mission. Despite this, a number of stages have Eggman's machines representing the hero alignment.
This level is set in the ruins of Glyphic Canyon, but in the air and with some changes to the layout.
If one looks closely at certain doors in this stage, they will see a symbol that appears to be the hummingbird Nazca Line; this (coupled with the name of the song ("Vast Nazca") from the cutscene before Shadow enters the Glyphic Canyon stage) implies that the Black Arms possibly have some connection to Nazca culture.