He is captured by Loghain – a simple enough mistake.
It takes them a month to find and free him, and when they do there is a little less of Alistair. Not physically, thank the Maker, though his back is a mess from the lashings. No, there is a little less smiling, less jokes and wit, less bickering with the witch... and that is enough to alert everyone.
It takes her five nights to get him to talk, and in the end it is Zevran who recognises the signs, who leads him beyond the campfire to the skirts of camp and regales him with horror stories, who listens to Alistair's story.
Within the first three days of his capture Loghain has found his sister and summoned her to the royal court. With freshly washed hair and a nervous smile she appears, and he tells her what he plans to do – not out of any sense of malice, but just so she understands what is about to happen. She accepts her part with dignity, though the large amount of gold sweetens the deal considerably. Within two hours he has escorted her to Howe's estate and shown her the dungeon – and Alistair watches with wide eyes as Loghain fucks his sister in front of him. There is nothing sweet or gentle about it, it is a simple tactic. It affects him – even though she cares not for him, he still prioritises her safety in his own mind, and he is horrified that Loghain would stoop to such a low and bastardly manoeuvre.
He cries. She is thrown out.
Five days later they are back, another show for him, and he breaks once more, big aching tears rolling down his mucky cheeks. She is led out, given payment, and sent on her way once more.
Three days later, she comes to the royal court unasked. Loghain is not gentle with her. Alistair weeps.
Four days later, there is a change in the air. She takes the money, though it is grudging, and the Hero of River Dane is left wondering.
Three weeks into Alistair's capture, Goldanna and Loghain make love in front of his cell, slow and sensual and as she cries out, a litany of soft moans and even softer words, the bastard prince's mind shatters.