Cities are systems of systems of systems. These are often viewed through their subsystems, e.g. transportation, retail, health, welfare, crime, finance, water, political, refuse disposal, and so on. Any of these subsystems has its own subsystems, without clear boundaries, but they impact on and are impacted on by other subsystems. Some things are at discernable micro-, meso- and macro-levels, with surprising interactions between those levels. They have multilevel dynamics, and new self-organised subsystems can emerge while existing subsystems can disappear, e.g. ghettos can emerge, bus routes can disappear. There can be problems from unexpected interactions between systems through overlooked connectivities, and problems can occur due to a lack of joined up government. New ways of understanding cities and their multilevel dynamics are needed. The theory of hypernetworks will be introduced as a necessary, if not sufficient, approach to providing practical policy-oriented ways of representing the bewildering complexity of cities as ever-changing systems of dynamic multilevel systems. The theory will be illustrated by plans to expand the new Dutch city of Almere.