note: This spoiler was based on the script unlocked after the initial playthrough of the Japanese version
Ico is thrown in and trapped in a coffin like structure in the castle by the villagers because they believe he is cursed. When the large doors of the castle closes, the rumbling it produces knocks the coffin off and it cracks open, freeing Ico. He stumbles around the castle and finds Yorda locked in a large cage suspending above a spiral staircase. He rescues her from there and together, they attempt to escape the castle.
While they travel through the castle, shadow figures appear and try to reclaim Yorda. After reaching the front entrance the first time, Yorda trips and the Queen appears and chastises Yorda. The Queen says Yorda will soon rule the castle and tells Ico to leave her here. The Queen then tells Yorda she won’t be able to survive outside of the castle.
Ico and Yorda reach the outer gates of the castle with a bridge connecting it to the other land. As Ico and Yorda run towards the bridge, the bridge starts retracting. Yorda trips again and she gets separated from Ico by the retracting bridge, each of them on the opposite side. Ico, unable to leave her behind, makes a leap to reach Yorda, but falls short. Luckily, Yorda catches Ico’s hand and attemps to pull him onto the bridge. The shadows engulf Yorda and she drops Ico.
Ico falls onto a series of hanging cages and must make his way back up the castle. He ends up in the throne room of the Queen. Yorda is standing still and it seems that she has been turned into stone. The Queen says, “Forget it... you’re too late. This body will soon perish... Yorda will be revived as my successor. That is Yorda’s fate... she will be the receptacle for my soul, so to speak. When she awakes, her memories of you will have vanished. Now put the sword down and leave this place. Yorda would have wanted that, too.”
After Ico defeats the queen, she reveals that Yorda can never leave the castle, even if the queen dies. There is a blast that knocks Ico unconscious and his horns break off. In the closing scene, Yorda picks Ico up and puts him on a boat and pushes it away from the castle. When Ico awakes, he is on the shore of a beach. He walks a little down the shore and finds Yorda just waking up by the water.