Special operations are a very sensible domain and are subject to several rules and regulations, both international and divisional.
The international part of the regulations is set in the "SO Directive". All rules written there apply to all special operations in the world. You can find the directive here : SO Directive.
Category B (combat operations, interceptions,...) can only be flown with proper permission, inside a special operations group (like the BeSOG). It can NEVER be executed by an individual. Special operations flights can be flown as OAT (operational air traffic) only if a military ATC is present, according to the divisional regulations (see below). Otherwise, they have to fly like a civil aircraft.
Each active division has a letter of agreement (LoA) regulating the divisional procedures.
You can find the Belux LoA here : Belux SO LoA
Pilots can fly OAT below 4500ft AMSL in uncontrolled airspace. In controlled airspace, OAT only with ATC approval. Otherwise, GAT procedures apply (civil rules).
Speed limits : below 2000ft AGL (low level) : 420kt over ground, 450kt over water. Above : Mach 1 (subsonic). In GAT, civil speed restrictions apply. Exception can be done for interception in coordination with Belga Radar (MIL ACC). OAT must always be VFR, under VMC conditions. IFR SO flights are considered as GAT.