The Prequel: Alistair's sex life before the blight, Ostagar, and meeting the witches of the Wilde aka how Alistair really lost his virginity.
Chapter 1: Mother Superior
Alistair was a troubled youth. Every time he got close to someone who could take care of him, and that he could rely on as a child he lost them. Losing Arl Eamon was a particular blow, in some ways worse than losing his mother, because of his age and the circumstances surrounding the events. His deep sense of betrayal made it very hard for him to heal and connect with superiors as well as peers. He was a child that required a lot of patience and discipline.
The mother superior of the chantry, though on the surface a hard and rigid woman, was in fact rather well placed in her role. She had the compassion and skills to see what roles were best for people, and how to best manipulate them for their own good. Alistair was of course quite a problem child, and a slippery fish in her book, but she did do the best she could for the lad as he grew into a young man.
She saw that staying still for him would always be a problem, and even though she didn't feel it appropriate to show the boy actual motherly affection and familiarity, she did care for the young man a great deal. He was constantly testing boundaries, in her opinion as a way to remind himself that he was in fact cared for and valued.
She would always respond to his outbursts and bad behaviour with punishments that pushed him to interact with others. If he was caught cutting class to go talk to the stable hands and pet the horses she would make sure he was part of the group going to market and doing the manual labour. Though dull work it required brawn, constant motion, teamwork, and afforded the boy a view of the outside world and new people to see and speak to.
He wasn't meant for the priesthood and the kinds of punishments that boys who were would only drive the lad from the only home he had left. She couldn't bear to see that happen to such a bright and shining star or a child. It was at times hard for some of the more academic priests and members of the clergy to see past the bad behaviour and mouthiness she knew, but their type of discipline would only lead to the boy being further hurt. She ensured as best she could that this would not happen.
There were of course the regular trials and hurts of boyhood, but those she felt she couldn't nor should protect him from. The best she could do was what any guardian could do. She provided the best emotional safety net she could. He might not be aware of it, but there really were a lot of caring people on his side.
Keeping him busy and out of trouble was practically a full time job in itself. As he grew older she saw that the more he was out of the chantry grounds working (as punishments or as direct chantry business) the happier and more focused he seemed to be. She firmly felt that Alistair striking out on his own and cultivating his own relationships in the community was a very good building block for him in adulthood. The chantry would never fulfil all of his emotional needs, or undo the hurts of his childhood. True friendship and love over time might.
As he began the transition from boyhood to manhood she pushed him towards being a Templar. This would put his body to work, give him focus, a clear structure to live and work in, and would see her still having a direct hand in his life. Being a Templar was something for war time or young men. She saw a life of hard work for Alistair, but one that would after his blush of being a young adult would afford him ability to make choices about the direction of his life, and perhaps even to marry and have a family of his own. Alistair was as close to a son as the Mother Superior would ever have.
To say the Mother Superior was livid when Alistair was conscripted by Duncan was certainly an understatement. She went as far to tell Duncan how much he was stealing from the young man, and all the other practical and emotional arguments a mother would make. It took all her self control not to break down and beg Duncan to take another. She knew Duncan could see her pain, but wouldn't budge. He took Alistair from the castle the very next morning. At least Duncan had torn the bandage away quickly. She mourned for many months after Alistair was gone.