While analysing the organisation of terrorism and studying its emergence and evolution, we must conclude that almost nothing about terrorism can be stated for sure, except that it is violent, unpredictable, and invisible. In short, terrorism is something asymmetric to everything we know. Focusing on the question of how to organise the Maritime Security System (MSS), this paper proposes a set of recommendations concerning MSS architecture, derived from an analysis of terrorist organisations. Basic considerations for the analysis are provided by analysing asymmetry in terms of countering terrorism. In conclusion, this paper presents a model for a harbour protection system, developed within a national project. The model explores centralising a network-organised MSS, at a level immediately above the terrorist threat level.