Mission critical systems (MCS) are complex nested hierarchies of systems, subsystems and components with defined purpose, characteristics, boundaries and interfaces, working in harmony to deliver vital organisational functionalities. Upgrading MCS performance is inevitable when capability enhancement is required or new technologies emerge. Improving MCS however is considered with certain degrees of reluctance due to their sensitive role in organisations and the potential disruptive impact of unexpected consequences of change. Innovation in MCS often appears in small steps that affect the entire system due to their highly interdependent structures. Effective management of innovation introduction in complex systems require systemic/systematic processes that involve process management and collective analysis, scoping, decision-making and R&D which relies on effective information sharing. This approach should run throughout the system and must include all aspects and stakeholders, utilising the skills and knowledge of all involved. This chapter describes the basic concepts and potential approaches that could be utilised to build intelligent systemic/systematic and collaborative environments for MCS innovation. Advances in ICT technologies provide an opportunity to access the wider sphere of knowledge and support the systemic innovation processes. Adopting systemic approaches increases process efficacy, leading to more reliable solutions, shorter development lead times and reduced costs.