Due to the really strange Development History of Ultima IX, there are numerous remnants of the original plot left in the game that in isolation make no sense. It was due to the hasty re-tailoring of the world that these things either were forgotten, ignored or put into a vastly different context.
Using the fly-cheat to get to the roof of Stonegate reveals that the roof had been completely constructed, with lightsources, a way down, a strange pattern on the ground looking like glyphs, and a teleporter to get into Stonegate itself. Most players would then wonder why the roof was created with so much detail if there isn't any way to get there in normal gameplay.
The answer to this question lies in the original Bob White Plot.
Here, the roof of Stonegate was intended for the big finale, where the Avatar and Lord British would have cast Armageddon to destroy the Guardian together with Britannia (he had linked himself with Britannia's life force) to end his reign once and for all. The strange glyph pattern on the floor would have lit up during the casting of the spell, thus why it is on the texture.
Another remnant is seen in the re-cut Armageddon video of the final game, which is used several times. In this video, Stonegate is seen right at the beginning for a second, pointing to the function of the roof in the original plot.
By the way, it seemed curious that the video was supposed to show the gypsies of Minoc being annihilated. There are ruins in the background that are found nowhere in Minoc. The answer lies in the fact that originally, this was the end video and showed Skara Brae, which indeed does have many ruins. (The part where everyone dies was created and added for the new plot.)
The Cathedral of Love
The Cathedral of Love in Britain had a more important role in the original plot. It was where the Avatar would meet and re-animate Shamino. Also it was used by Amoranth as his headquarters. Amoranth also had a much bigger role in the original plot as one of the leaders of Britannia. During the re-design of the plot, practically nothing was left of these plot-points, leading to the cathedral having a more secondary role.
After the Avatar got captured by Blackthorn, the video continues by showing him being thrown into a cell in Deceit. Does it? Strangely enough the cell in the game looks nothing like the cell in the video. Also, the quality of the video seems to degrade a lot between Blackthorn closing Samhayne's door and the Avatar arriving in prison.
Actually, there are two videos, the second played immediately after the first. The second video is from the original plot (thus the lower quality since it's older) and in reality shows the Avatar being thrown into dungeon Wrong after being lured into a trap by Blackthorn when trying to expose his dealings. The original version of the video also showed Lord British within the cell, as he was viewing the scene through a message from the Guardian.
The expensive video had to be used so the plot was changed to fit it, but the cell obviously wasn't changed for it.
Shrinking the whole game created lots of maps that no longer had any use in the game. However, they are still in the game, although it takes some effort to reach them. Once found, some really interesting things appear that show some of the cut content.
The topic is so complex, it has it own page: Unused Ultima IX Maps.
In the game, the Avatar finds a mirror hanging in Lord British's bedroom that looks exactly like the Guardian's Mirror of Darkness. It is rather useless and only shows the Armageddon video, before breaking. Also no one mentions it or why it was there in the first place.
This of course raises the question why it was there in the first place.
It actually is a remnant form the original plot. In it, the Guardian had somehow made Lord British hanging the mirror into his bedroom and used it together with his own mirror on Terfin to send Lord British nightmares to turn him hostile against the Avatar. This is also probably why the Avatar gets karma for destroying it.
Of course the karma gain makes no longer any sense, with the nightmare-plot removed.
The answer why this was done lies in the really expensive cut-scene that had been created. Originally it showed a dream of Lord British where the Guardian tells him a lie that the Avatar summons Pyros to destroy Pagan and gets destroyed himself in the end.
In the end they re-cut the video to remove any reference to Lord British and the dream and modeled the area on the Isle of the Avatar to look like the video, just so that they don't have to throw it away. They didn't entirely succeed, for a second the wall of Lord British's castle (he sees the whole thing in his dream from the castle balcony) can be seen in the background.
It always seemed strange that the dungeon Hythloth had suddenly mutated to the sewer system of old Magincia while in all games before it had been a decaying mine on the Isle of the Avatar. The answer lies in the fact that the dungeon in question actually isn't Hythloth!
Indeed, it actually is the sewer system of Britain. Since there had been no time to create Hythloth, this hasty solution was found and a room with the column added in so that the glyph-quest could be fulfilled.