The Handler's relationships are key. If in the fanfiction she forms an unexpected bond with one of the Umbrella Academy members, it can be a turning point for her character. Maybe she starts to see the value in the Academy's unorthodox ways and questions the Commission's strict regime. This new relationship could force her to re - evaluate her loyalties and goals, creating a believable and engaging character arc.
A great plot could be that The Handler gets amnesia. Losing her memory, she has to rely on the kindness of the Umbrella Academy members she once opposed. This forces her to see them in a new light and also makes her question her own actions. It could lead to a journey of self - discovery for her within the world of the fanfiction.