From Sonic Retro
GUN Fortress is GUN's top-secret base in the United Federation and the name of a level in Shadow the Hedgehog. It is rumoured to be an underground base as Rouge the Bat comments that GUN Fortress is subterranean.
If you've 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 show that the Black Arms mean serious business. Nothing is left of the United Federation's former capitol but a smothering crater, though all of its residents have been safely evaluated beforehand.
If you've completed Air Fleet's dark mission, the President escapes within an inch of his life of 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 G.U.N. Commander assures him that their forces will rally. Unfortunately for the humans, over a thousand alien invaders have managed to breach the fort's outer defenses, including stark raving mad Shadow.
Either way, things aren't looking so great for humanity in their struggle against the Black Arms. G.U.N., the only real force capable of mounting a competent defense, has been reduced to besieging what remaining forces it has at its center of command. 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.
If you're misanthropic to the core and help the Black Arms in destroying the mother computers, Sonic the Hedgehog and the G.U.N. Commander (piloting the prototype battle robot Diablon) confront Shadow in Earth's absolute last stand. Defeat them and Shadow will finally acquire all seven Chaos Emeralds. The fallen Sonic asks what Shadow plans to do, and Shadow replies with his intention to dispense justice to humanity by destroying their planet. Cue maniacal laughter, screen fade, credits.
...Or you could atone for your wicked ways at the last minute by securing the final Chaos Emerald from the Black Arms. Black Doom is quite cheesed off by your impromptu treachery and intends to personally teach you a lesson. After you defeat him, a weakened Black Doom promises that the Black Arms aren't finished. In the most grandiose one-up of all time, Shadow retorts that he plans to use the seven Chaos Emeralds to take his rightful place as the ruler of the entire universe. Cue maniacal laughter, screen fade, credits.
- Hero: Rouge the Bat: Protect the fortress from the Black Arms.
- Dark: Black Doom: Destroy the Mother Computer and annihilate Earth once and for all.
^^^UNDER CONSTRUCTION, OBVIOUSLY. BUT FEEL FREE TO ADD TO THIS^^^