Modern systems engineering projects have moved from the development of new virgin, standalone products, to the upgrade and adaptation of existing systems to new capabilities. Enterprise systems are in a state of flux as new capabilities and improvements are implemented over time. They are characterized by complex technology acquisition and supply chains, variable, overlapping timescales, and numerous asset management and maintenance processes all whilst dealing with the pressures of minimal system downtime, maintaining operability and safety, and providing a reliable service. The organisations within the enterprise delivering these capabilities will evolve over time in order to meet these challenges. Whilst enterprise architectures are commonly used to manage the complexity and plan/design the strategic, operational and technical views in detail, attention to the holistic, organisational aspects is oft considered to a lesser degree. This paper demonstrates how Model-Based Systems Engineering principles can be used to manage the complexity of the introduction of new capabilities from an integrated organisational standpoint.