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This paper discusses the instructional design experiences and processes shared by a multi-disciplinary group—including more than a dozen faculty, staff, and students—while developing a series of online courses on Model-based Systems Engineering (MBSE) for professional engineers, a project sponsored by the National Science Foundation. The team size, the complexity and uniqueness of the subject matter, the targeted learners, and the pre-determined research questions created a rare situation in which the team members collaborated and/or negotiated outside the realm of the traditional instructional design process. Over time the team went through two different types of instructional design processes, beginning with a waterfall-type process where the communication between the subject matter experts (SME) and the design team was somewhat limited and finally evolving to a collaborative process where the interaction between the two teams was more direct and immediate. The evolution of the design process and the dynamics between the SMEs and the design team resulted in several major design revisions implemented to improve the quality of the online courses.