The Inner Sanctum
The Inner Sanctum is Abalach-Re's experimental facility not only does she conduct her experiments here, but she also keeps important prisoners here for interrogation. Hardly anyone save Abalach-Re's creations has left his place alive. The reason is not only the Queen's method of torture, but the simple fact that the building itself is alive and hampering potential outbreaks. This is also a secret that Abalach-Re seeks to protect. The Inner Sanctum is the result of the monarch's studies and of rhulisti life-shaping techniques(see Windriders of the Jagged Cliffs). Abalach-Re merged the life-shaping with defiling magic and created life-shaped abominations, one of which is the Inner Sanctum. Prisoners in the Inner Sanctum are guided naked into one of the many cells where they are held up against one of the walls by the kuotaghas. Immediately, the wall begins to insert tentacles into the prisoner's body. These tentacles are not only chains, but tubes which administer tranquilizers and other drugs, recycle the prisoner's bodily waste and deliver nutrients and moisture so the victim is kept alive - until the Queen allows the wall to consume the prisoner, which it usually does by inserting an acid which liquifies the victim's body.
The Inner Sanctum has a similar function when it comes to the experimental labs. Here, slabs and floors absorb blood, hold prisoners steady, administer drugs (if you are lucky you get an anaesthetic) and even provide different kinds of temperatures and illumination.
The Inner Sanctum may get so greedy for 'food' that the Queen has trouble controlling it. This can have several consequences. The PCs could be prisoners and have a chance to escape the Queen while she fights with the Inner Sanctum. Or she might even enlist the PCs in her efforts to control the Inner Sanctum.
The Yellow Monastery
The Yellow Monastery used to be a place of more passive resistance. The monks condemned aspects of Abalach-Re's rule (such as slavery, violence) mainly for spiritual reasons. Since the death of Abalach-Re, the Monastery has become more active, first focusing on creating stability and offering protection in its surrounding area, and later by a series of smaller interventions. In contrast to some more radical resistance organisations, the Yellow Monastery tries not to succumb to violent ways.
This has enabled them to remain in the open, virtually unchallenged. Unlike members of the resistance, they are not perceived as a threat. However, freedom fighters have been cared for by the Yellow Monastery and although it is suspected, no one has been able to prove it so far.
What has also helped these monks is their eloquence. Even if they are accused of something, they have so far always been able to talk their way out. How long they will be able to keep this up is uncertain, although their current leader Shantaru (19th level psion) is not to be underestimated...