The Queen

The Queen is the ruler of the castle in Ico. Shadowy and imposing, her goal is to extend her own life by possessing her daughter, Yorda. Previously, she had relied on the life of the children placed in the sarcophagi, but Ico's escape (and subsequent rescue of Yorda) threatened both plans. She therefore stops at nothing to try and separate Ico and Yorda, mostly through her minions of shadow creatures. She only directly confronts Ico and Yorda twice, and both times they are dangerously close to escaping her lair.

Analysis

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.
It suggests that she is creating the portals through which the Spirits appear. Since she is able to project this attack through one of them, it makes sense that she created the portal in the first place and controls it. It also seems unlikely that beings as limited as the Spirits could have created the portals anyway. As with her other powers she is able to create these portals throughout the Fortress, but the varied time between the Spirits' attacks suggests that she is not able to keep it up constantly, further supporting the idea that her powers are weakening with age.

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.
Assuming she would not, the reason would be that she did not need Yorda dead at that point and thus preferred to recapture her instead. The Queen could have killed Yorda at any time, but chose not to, either because she simply did not want to, or because she needed to keep Yorda alive until the right time. In this case, when Ico and Yorda's escape was prevented by the Orbs the time was right to petrify Yorda, and so she appeared on the bridge.
Assuming she could not, the thing preventing her from killing the pair all along must have been Yorda's own power. It is displayed many times in the story that Light Magic like Yorda's power is very destructive to Dark Magic. Specifically, the statues in the Throne Room and the Sword are able to completely block the Queen's attack within a small area around them. Since Yorda commands powerful Light Magic, it is possible that her very presence prevented the Queen from attacking the pair directly. In this case, when Yorda was struck down by the Orbs she was greatly weakened, due both to the Orbs' attack and the effort of opening the Main Gate, and must have been so weakened that the Queen was finally able to use her powers directly.
It is of course possible that the truth is a mixture of these two, for instance that the Queen could not use her powers on Yorda until she was weakened, but that even if she could have she would not have killed Yorda until that time anyway. Whatever the exact truth, the reason the Queen sends the Spirits to retrieve Yorda seems to be that the only way she can intervene directly is to kill Yorda, which for whatever reason is not an option until their encounter on the bridge.

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 obvious from the condition of the Fortress that it is an ancient place, however it is possible that it is even older than it appears, and that it is the Queen's power that has been holding it together when it should have fallen into the sea. The Queen demonstrates that her powers include large scale telekinesis when she closes the main gate, the first time Ico and Yorda reach it, and the appearance of the portals throughout the Fortress suggest that her powers extend throughout it whether she is physically present or not. It is possible that during the story she is actually using the majority of her remaining power to keep her domain intact. As she got older her body deteriorated, her powers weakened, and thus parts of the Fortress became damaged and inaccessible. When she finally died, the power holding the Fortress together disappeared and it suddenly fell into the sea.

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. Further discussion of this, and of the alternative idea that the Queen was always a Spirit, requires discussion of her, Yorda, and the overall plot, so I will keep it for a separate section.