There are three ways to access Sky Troops: Shadow must either help Amy find Cream and Cheese in Cryptic Castle; collect the Chaos Emerald from Prison Island; or repel the G.U.N. attack on Eggman's Circus Park. Whatever the method, Sky Troops' preceding cutscene shows Eggman reviewing images of Westopolis' invasion with mounting rage. In the next scene, Shadow is at Black Doom's side, standing upon one of the floating aliens ships. Doom boasts that his armada is over 2,000 years old, and that it is "The perfect killing machine... ready to impose terror in unimaginable ways!". His hyperbole is, however, cut short when, on the horizon, the piscine orange ships of the Eggman Fleet appear.
As battle is waged between the two villainous armadas, Shadow has three options. In the Dark mission, he can side with the Arms and shoot down Eggman's cruisers using the fixed-position cannons scattered about the ruin-ships. In the Normal mission, Shadow simply heads directly for Eggman's flagship to confront the fat man personally. In the Hero mission, the hedgehog follows the suggestions of Eggman's floating drone and sabotages the alien ships from the inside by blowing up the power-cores he activated in Glyphic Canyon.
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.
Behind the Secret Door in this stage, there is a Black Volt, an Elite Black Hawk fitted with armor and a worm launcher. Shadow can tame it to ride it along the rest of the stage. The worm launcher makes it easier to collect item boxes along the way.
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, number of stages will in fact have Eggman's machines representing the hero alignment.
This level is very similar to Glyphic Canyon, but it's in the air and has a few other changes.