Traditionally, a driving goal of digital storytelling is the generation of dramatic stories with human significance, but for learning purposes, the need for drama is complemented by the requirement of achieving particular learning outcomes. This article present an interactive storytelling conceptual model aiming on managing emergent narratives based on pedagogical goals. This process is supported by the adoption of a narrative hierarchical structure based on plot pieces that establish the relationship between competences and game mechanics. These structures are match with the current plot unfold in order to support the guidance process that is done through an innovative narrative mediation protocol called Collaborative Negotiated Deliberation (CND). CND supported the deliberation in different deliberation layers and taking into account time. In addition a case study is described where the concepts presented throughout the paper are applied and exemplified.