The Longest Journey[]
The seat of the Guardian is located in the Tower, a mysterious structure in the Guardian's Realm. Only 'the Guardian who was, the Guardian who is, and the Guardian who will be' can gain access to the Tower. It was originally built to channel the energies that created the Divide, to preserve the Balance of the Cosmos (as Vestrum Tobias puts it) while separating the two worlds. The Guardian's Realm appears to have been created around the Tower itself when the Divide was born.
Suspended above the desert of the Realm, the Tower has no visible markings or architecture: it is just a pendulum of stone, several hundred feet high. At its base is the Well of Making. Beyond that, in the abyss below is, as Crow reported, quite literally, nothing. There is no means of access to the Tower from the desert - finding a means across was April's Trial of Matter. She used water from the Well of Making on the Nothing below, and a bridge was created.
The only way to get into the Tower from April's point of view is to reassemble the Stone Disk and place it at the base of the Tower. A Guardian's touch is needed to open the way, elevating the ground beneath to lift the potential Guardian towards the Tower.
As far as the Tower's interior is concerned, the bottom of it is actually hollowed out, allowing the Guardian to ascend inside, but as for the rest of it, we only see the Guardian's throne room. In the centre of the room is a device that appears to create the flow of the Balance through the Guardian. We first see Adrian when he is suspended beneath it, with a stream of white light running through his body.
On the back wall are two enormous stone dragons in an ouroboros pattern, that in the normal course of events are eternally but steadily devouring each others' tails. When Adrian left the Tower, one of the dragons accelerated its devouring. When she entered the room, while the Balance was failing, April commented that this dragon had almost completely consumed the other. This suggests these two dragons represent the current balance of order against chaos and magic against science.
On another wall is a huge, ornate stained glass window shaped like a burning eye. Presumably there is another window on the other side that is identical: these windows may represent the Guardian's fair and impartial perception of the two worlds. When April leaves the Tower and looks back, she sees two energy streams emerging from either side of the Tower, from some sort of orifice at its peak.
Dreamfall[]
When April Ryan returns to the Guardian's Realm, among many other changes is the fact that the Tower has fallen from the sky and now lies in ruins. She comments that she likes what Gordon Halloway has "done with the place", so the collapse of the Tower may also be his doing. Although we know Gordon is prophesied to be the last Guardian of the Balance, this still seems like an ominous development. The Tower was in place for twelve thousand years and was, in a lot of ways, the closest physical analogy to the Balance itself. Its fall seems significant.