The last decade witnessed a gradual shift from cloudbased computing towards ubiquitous computing, which has put at a greater security risk every element of the computing ecosystem including devices, data, network, and decision making. Indeed, emerging pervasive computing paradigms have introduced an uncharted territory of security vulnerabilities and a wider attack surface, mainly due to network openness, the underlying mechanics that enable intelligent functions, and the deeply integrated physical and cyber spaces. Furthermore, interconnected computing environments now enjoy many unconventional characteristics that mandate a radical change in security engineering tools. This need is further exacerbated by the rapid emergence of new Advanced Persistent Threats (APTs) that target critical infrastructures and aim to stealthily undermine their operations in innovative and intelligent ways. To enable system and network designers to be prepared to face this new wave of dangerous threats, this paper overviews recent APTs in emerging computing systems and proposes a new approach to APTs that is more tailored towards such systems compared to traditional IT infrastructures. The proposed APT lifecycle will inform security decisions and implementation choices in future pervasive networked systems.