The Forces of Light and Dark in Ico
The will behind all the events in and around the fortress is the Queen. A mysterious figure whose mere existence seems unknown even to those who sacrifice their children to her, her identity and history are never revealed. All that is known is her desire to continue living, whatever the cost.
The Extent of the Queen's Powers
Throughout the story the Queen demonstrates powerful magical abilities, however the fact that she never attempts to stop Ico and Yorda herself suggest limits to these powers. Her objective throughout the story, as far as we know, is to return Yorda to captivity. She has the power to exert physical force on the Fortress, seen when she closes the Main Gate, and she has her magical attack which will kill whoever it touches, but to return Yorda to the Tower seems to be beyond her. She states herself that her body is dying, and this may explain why she seems to be limited to a few of powerful magical abilities. It is quite possible that due to her weakened body she is like Yorda in that she has significant magical power, but is much less adept at physical tasks. Thus it is probable that the reason she sends the other Spirits after Yorda is that they are more suited to physically forcing her back to her cage.
Aside from her apparent telekinetic abilities, her main power is the wave of darkness she can project, which will kill anyone it touches by petrifying them. This is usually only seen in the final battle between Ico and the Queen, however, if you allow Yorda to be captured during the course of the game, that same wave of darkness appears from the that portal Yorda was pulled into and kills Ico. This tells us a number of things about the Queen and her powers.
Returning to the Queen's motivations for not going after Yorda more directly, we are still left with a puzzle. The one factor which has not been taken into account yet is that when Yorda is finally stopped on the bridge by the Orbs, the Queen turns up and uses her magic to kill her. Why would she enlist the Spirits to recapture Yorda, if she was capable of killing her at any time, and intended to kill her anyway? If Yorda is captured during the game the Queen uses the attack to kill Ico once Yorda is fully through the portal. Therefore it must be Yorda's presence which prevents the Queen from attacking before they meet on the bridge. There are two possible reasons why Yorda's presence would prevent her from attacking; either she could not attack, or would not.
The Queen & The Fortress
The Queen's relationship to the Fortress is never explained beyond the fact that she is referred to as the 'Queen'. She obviously has control over it, but that is not difficult since only she and beings that appear to be under her direct control inhabit it. Looking beyond what is directly presented, there is a parallel between the physical condition of the Queen and that of the Fortress. The Queen's body is deteriorating due to its age, and the same is true of the Fortress. This parallel is easily explained away by the fact that both the Queen and her home are very old, except that when the Queen dies the Fortress also 'dies'. This suggests a stronger link between the two than is immediately apparent.
It is unknown exactly how much power the Queen has over the Light Magic aspects of the Fortress. The fact that she is a Spirit would suggest that she could have no interaction with Light Magic devices, but we know that she used the Casket Chamber to resurrect Yorda, and it is quite possible that she was responsible for the Orbs attacking Yorda. If the Orbs are intended to attack Spirits when activated, she must also have some way of preventing them from attacking her. So, despite being a Spirit, she must have some power over the Fortress. It may be noteworthy that in both of these cases, the Casket Chamber and the Orbs, she is activating a device which was already prepared to activate. She never shows any ability to directly interact with Light Magic devices as Yorda does, nor to deactivate them, even when Ico and Yorda are using them to escape.
The Queen's True Nature
There is a conflict in the story in that the Queen is the ruler of a Fortress which is based on Light Magic, which opposes Dark Magic and Spirits such as herself. This same conflict occurs between her and Yorda, the person who is supposedly her daughter is a Light Being, in alignment with the Fortress against her mother. This tells us that the Queen is more than just a powerful Spirit. Since we have already speculated that Dark Magic is related to the dead, and towards the end of the story we see Yorda brought back from the dead in a near identical form, it is not a huge leap to conclude that the Queen herself was once a Light Being. This idea is supported in her physical appearance, she has a humanesque face, and she bears a striking resemblance to Yorda, suggesting some link to a Light form of her own.