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Central City lies in ruins, despite the best efforts of Knuckles and G.U.N. to reduce the damage by defusing the Black Arms' explosives. The Eggman Fleet has been decimated during a confrontation with the Black Arms' fleet, and Black Doom has shown Shadow his past destroying one of GUN's most powerful machines. The future looks bleak for Earth. High in the skies of Earth, G.U.N.'s flying battleships are evacuating from Central City. At Central City, in the White House, the Commander arrives with two of his men and urges the President to evacuate to a more fortified position to protect themselves from the advancing Black Arms, which the President reluctantly agrees to after some encouraging words from the Commander. Shadow and Black Doom stand outside the building as they watch the President escape towards the G.U.N. flying battleship holding position overhead. Black Doom orders Shadow to follow the President (which the player can choose to do or not). Shadow then skates off towards the battleship that the President's escape pod is going to as it begins to depart.
Immediately upon boarding the battleship, Shadow runs into Tails, who asks for Shadow's help in protecting the President's shuttle from the Black Arms' boarding parties by defeating all the aliens. If Shadow chooses to side with Black Doom instead, he must destroy the shuttle, which is being conveyed on a monorail track through the ship, before it reaches the safety of a secure hangar in the ship and is unable to be pursued further. Alternatively, Shadow can simply pursue for the Chaos Emerald located in the ship.
The best chances to hit the President's ship is when it is rotating along the rail or when you have access to a cannon. To get an A ranking, you will need to finish it off before it gets to the end. Or, you can burn through the stage, and try to destroy it on the final elevator. If you have been damaging it throughout the stage, you will at least pass the Dark Mission for this stage.
Use Chaos Control in areas where more jumping than running is required.
Throughout the Facility, there are fans that will try to blow you backward. To keep from being blown away, grab on to the bars and hang on until the wind stops. After the wind stops, Spin Dash forward and jump over the laser turrets to exit the area.
You can't grind along the electrified rails, because they are electrically charged! The only way you can do this is with an Air Saucer. Alternately, you can fill your gauge up and grind while you are invulnerable. These electrically charged rails save a little time, but more importantly, they often lead to a weapon cache.
The first trouble spot occurs after the third Checkpoint. Once you are outside of the facility, you will see moving platforms. Jump across to the third one. Spin Dash along the wall between the lasers, and grab onto the pole and climb up. It is fairly simple to do, but at least a couple of you will fall at least once.
Behind the door is a Black Arms Air Saucer. When mounted, it enables Shadow to grind along the electrified rails safely. The rails lead to a secret room filled with weapons (including a 'Shadow Crate'), extra lives and a health unit for the vehicle. The saucer can be used all the way through until the end of the level, but this will require some careful riding. A helpful tip: if you want to complete the level with the saucer or reach other electrified rails further along the level, double jump continuously when there is a steep slope to overcome them.
Even after the escape pod is destroyed, in the GUN Fortress stage, it appears without a single dent or scratch from the mission.
When Doom's Eye says "This shall be the last time that the humans ever see the sun" during this stage, he might be foreshadowing how the Black Comet will be teleported down to Earth and launch its attack during the Last Story.
There are multiple paths to this stage in which Shadow never even sees Eggman, yet he still comes to the conclusion that he is an android if the player does the Hero mission.