Creation

The Age of X storyline featured many parallels to the continuity of the mainstream Marvel Universe.  Writer Mike Carey created a sequence of events whereby mutants were all called to live together.  However, instead of relocating to Utopia under Cyclops' rallying call of unity, in this alternate timeline Magneto offered a santuary for all mutants in Fortress X. 
  

Story Arcs

 

Prior To The Age Of X

Fortress X made it's first appearance at the end of X-Men: Legacy #244.  For the entire issue, Blindfold had been searching for a malevolent force.  Due to the complicated nature of her powers, she believed that someone was hiding who would change everything for the worse.  After a process of elimination took her on a tour of the island of Utopia, she was confronted by the looming shadow of Fortress X.  None of the other X-Men were able to see the tower.  However, it foreshadowed the start of the Age of X story arc. 
 

Age of X

For the duration of the Age of X, Fortress X was both a home for the last surviving mutants and a symbol of their desperate fight for the right to live.  It towers defiantly above the bleak surrounding landscape, echoing the defiance of the mutant residents who refuse to succumb to the laws that would execute them.   
  

Architecture

Foundation
Although it largely looks like it was made from rubble, Fortress X was constructed from many famous New York City skyscrapers (including the iconic Chrysler Building).   Magneto took hold of the ironwork in the buildings, and used that to steal the skyscrapers, relocate them and reconstruct them.
  

Outside & Outer Walls

The areas around the Fortress are mostly wasteland. A 'No Man's Land' razed to the ground with any previous landmarks destroyed from the thousands of battles between humans and mutants.   As the land is mostly flat  battle damaged, the looming shadow of Fortress X literally towers above everything else.
 
Closer to the Fortress are remnants of 'civilisation'; posters warning humans to report mutants in and up-turned cars.  It was around this area that Legacy was walking when she had absorbed Tempo's life, and where she observed Katherine Pryde hiding a digital camera. 
 
Dr Kavita Rao established a medical area on the inside of the peripheral walls.  Dazzler questioned the logic of having an area for the sick & wounded so close to the battlefield, yet it reduces time to transport patients.  It is nearby here where the mutants like to gather around campfires, telling stories as they prepare for the oncoming battles. 
 

Inside

The Fortress is like a city in the sky, with many stairways and streets weaving between residencies & communal areas.  There are private dormitories for each mutant, or each couple.  These are home, providing warmth & privacy such as that enjoyed by Basilisk & Frenzy.  There are also places for mutants to unwind after battle, including (but not exclusive to) Wolverine's bar the Rat Run.  Here mutants can drink and play cards. 
 

Administration & Incarceration

As the General of the mutant forces, Magneto oversees all movements inside & all around the Fortress.  He has a grand observation room with a hanging pillar of monitors.   
 

  Access is restricted to most mutants, but even Magneto's closest allies are excluded from the Brig.  Even Fortress X holds mutants prisoners.  Magneto's propaganda lets the mutants believe that some of their own kind are so dangerous that they must be kept locked up or safety. There, Danger monitors the movements & the security of the holding cells, while X monitors the life-signs of their prisoners.  Danger even questioned Magneto's access, when he returned Pryde to her solitary confinement. Aside from Pryde, it seems that the majority of prisoners are telepaths who have been mechanically neutralised. 
 
Parts of the Brig were constructed from high security bank vaults.  The maximum security prison is located dozens of stories above ground.  Therefore when Legacy was fleeing from Danger, she was forced to leap through a window.  It was observed that her body wasn't found on the floor, suggesting that the Brig is located above the regular residential areas.