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GUN Fortress is G.U.N.'s top-secret base, featuring as a level in Shadow the Hedgehog. Built in a series of underground caverns, it houses the three Mother computers that coordinate those remaining forces resisting the Black Arms invasion with replenishing GUN with dozens of GUN Troopers, Giga Troopers, and BigFoots. In addition, it is armed with surveillance cameras and an immeasurable number of GUN infantry and machines. It is located in a mountain near the sea, as seen on the platform where the goal ring is located.
If Shadow has completed The ARK's dark mission and deactivated Space Colony ARK's defenses, the Black Arms take advantage of the opportunity and seize control of the Eclipse Cannon. After Black Doom telepathically broadcasts a speech demanding the surrender of Earth's forces, the Eclipse Cannon is fired at Central City to demonstrate the power that the Black Arms possess. Nothing is left of the United Federation's former capitol but a smoldering crater, though all of its residents have been safely evacuated beforehand.
If Shadow has completed Air Fleet's dark mission, the President barely escapes the would-be political assassin Shadow the Hedgehog. The rather flustered leader is taken to the deepest part of G.U.N.'s subterranean headquarters, where the Commander assures him that their forces will rally. Unfortunately for the humans, over one thousand alien invaders have managed to breach the fort's outer defenses, including Shadow.
Either way, things aren't looking so great for humanity in their struggle against the Black Arms. G.U.N., the only real competent defense force left on the whole of Earth (Eggman included) capable of fending off the Black Arms, has been reduced to barricading what remaining forces it has at its center of command where it can keep resupplying its mechanized forces quickly. Shadow is tasked by Doom's Eye to destroy the three mother computers which churn out G.U.N. robots. Taking an uncharacteristic change of heart, Rouge the Bat is determined to prevent the Black Arms from swiping the last Chaos Emerald that lies at the end of the base. It's your choice whether to aid Doom's Eye or Rouge.
Helping Rouge and allowing GUN time to regroup results in Black Doom confronting Shadow in person over his last minute betrayal, while helping Doom's Eye in crushing the last bits of human resistance leads to where Shadow is confronted by the GUN Commander in person in the incomplete Diablon alongside a furious Sonic, making a heroic last stand to stop Shadow and Black Doom at all costs.
The following weapons can be found in GUN Fortress:
From the start of stage, it is located on the left side behind the large container.
After using the pulley in the first large room, get the key that is located to the right between two large containers.
In the second large room after getting the Jump Vehicle, go up to the second level past the pulley, and find the key sitting on the ground next to the barriers.
The key is located behind the second core after the fourth Checkpoint. This one is easy to miss, especially if you are going for speed.
After Using the pulley to go up after the secret door, you will arrive at a hallway with two walls on either side. Use the triangle jump to get past the three laser beams at the end, and land in the area with the key
Destroy the core of the base!
Destroy the three cores.
There are gun turrets in all three core rooms for use. If there are no enemies Shadow will automatically target the "cores" himself. Also, attacking the enemies will quickly fill up your Dark Gauge. Killing all of the GUN soldiers/mechs and causing lots of destruction without dying will give you about 40,000 points in total, more than enough for an A rank. This makes it one of the few Dark missions where you don't need a time bonus to get an A rank.
This secret door can be found while running on the normal path of the stage, just behind a Big Foot. Inside, there is a G.U.N. vehicle. You can either take it and drive down the path ahead, or have Shadow go on foot. You will get many rings and extra lives. The shortcut also bypasses a difficult area regarding a pulley and dodging laser barriers and G.U.N. soldiers above a bottomless pit before rejoining the main path that leads to the third and final mother computer and the Goal Ring.
Ingame files refer to this stage as bas02, possibly short for BASE while the 02 signifies it is the second GUN base themed stage (with Air Fleet being the first, signified by its filename bas01).
According to Rouge, the electrified looking pools of blue seen throughout the fortress is Toxic Waste. Doom's Eye can also comment saying that the contaminated stream will probably eat away at (Shadow's) flesh and bones.