Central City lies in ruins. The Eggman Fleet has been decimated, Black Doom has shown Shadow his past destroying one of GUN's most powerful machines. The future looks bleak for Sonic's world. High in the skies of Sonic's world, G.U.N.'s flying battleships are evacuating from Central City. At Central City, in the White House, The Commander urges the President to evacuate to a more fortified position to protect themselves from the advancing Black Arms, which the President reluctantly agrees to. Shadow and Black Doom stand outside the building. Black Doom orders Shadow to follow the President (which the player can choose to do or not). Shadow then skates off towards the ship where the escape pod is going.
Immediately upon starting the stage, 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. Shadow can switch the rails in places where the path forks to send the pod into dangerous Arms-controlled regions of the ship, but it is generally up to the hedgehog himself to deal massive damage to the vehicle; as such, the Shadow Rifle is a good choice of weapon for this mission.
After using the pulley to go up above the secret door. Triangle Jump through the hallway and enter through the top door.
On the first junction, take the danger path, and destroy the containers on the left side of the room with the appearing GUN Trooper to get the key.
After the third Checkpoint, it is located in the large circular room. You have to use you Spin Dash on the red slime to reach the upper level where the key is.
After the fourth Checkpoint, take the safe path, and destroy the container next to the first GUN Turret.
It is after the seventh Checkpoint in the large circular room on the top level between two large GUN containers. Once again, you must use the Spin Dash on the red slime to reach the top.
Destroy the President's ship before it reaches the end.
Flip the switches to the red position to lead the ship into unprotected areas. It is best to attack when it is turning. Use the level's cannons and turrets when they are available.
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 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 beams 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. Or 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. 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.
Prima Official Game Guide for Shadow the Hedgehog
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.