Model-Based Systems Engineering aims at creating a model of a system under development, covering the complete system with a level of detail that allows to define and understand its behavior and enables to define any interface and workpackage based on the model. Once such a model is established, further benefits can be reaped, such as the analysis of complex technical correlations within the system. Various insights can be gained by displaying the model as a formal graph and querying it. To enable such queries, a graph schema needs to be designed, which allows to transfer the model into a graph database. In the course of this paper, we discuss the design of a graph schema and MBSE modelling approach, enabling deep going system analysis and anomaly resolution in complex embedded systems. The schema and modelling approach are designed to answer questions such as what happens if there is an electrical short in a component? Which other components are now offline and which data cannot be gathered anymore? Or if a condition cannot be met, which alternative routes can be established to reach a certain state of the system. We build on the use case of qualification and operations of a small spacecraft. Structural and behavioral elements of the MBSE model are transferred to a graph database where analyses are conducted on the system. The schema is implemented by an adapter for MagicDraw to Neo4j. A selection of complex analyses are shown on the example of the MOVE-II space mission.