Learning in complex and ill-structured knowledge domains requires accommodation of multiple perspectives embedded in authentic activities and the reconciliation of those perspectives with personal beliefs resulting in conceptual change. Cognitive flexibility hypertext systems support that process by enabling learners to explore authentic cases from multiple thematic perspective. Study 1 showed that knowledge exploration alone is insufficient to engage those conceptual change processes. So we reasoned that providing learners with environments that engage more constructive, personal knowledge representation activities would better support conceptual change. However, these environments rarely support learners in structuring, integrating, and representing their personal beliefs with other perspectives. That became the goal of our iterative research process. We describe a design-based research study conducted over three years that chronicles the evolution of a hypertext information system into a collaborative knowledge construction environment. Situated in different subject areas and contexts, the project examined learner roles for interpreting and later representing and constructing their own complex, non-linear content structures. At the core of the project was an evolving hypertext authoring system, Crisscrossing, in which users in the latest version collaboratively construct non-linear hypertext structures as well as represent non-linear and sequential pathways through the content structures they construct. During each research cycle, we conducted extensive usability testing and utilized qualitative and quantitative research methods to describe changes in learners' roles and their effects on students' conceptual change while interpreting cases and producing and annotating their own cases. Learners consistently produced patterns of artifacts within and outside the environments, experienced poor transfer to new cases, and manifested difficulty in accommodating and creating multiple perspectives and applying causal reasoning. Implications for system design are discussed.