I think it's the room "Proof of Existence" and the Organisation XIII 'graves' inside it.

One remaining with eleven dark lights, - After you've defeated Saix and Luxord only Roxas' stone is glowing, I assume Zexions isn't counted as it's destroyed.
Another goes out with every mortal fight. - When an Org13 member is killed, the light on their portal goes out.
Why just a year ago we were all shining bright, - A year ago was before th event's in CoM and KH2, so all of Org13 would have been alive.
But the memories can fill you with fright. - I suppose Sora would be a bit frightened due to his convoluted memories.
Take another step no more,
For we shall guard this sacred door. - You need to put Saix and Luxord's lights out before you can progress further.