The study looks at the conduct of military operations in relation to civilians in the communities they impact. Counter terrorism is viewed in reflection of the changing nature of war from classic mechanizations of combat on the battleground. I aim at answering the broad question; What if any is the correlation between foreign military assistance and terrorist activity in Kenya? As typical of qualitative studies I will rely heavily on experiences of individuals and groups of people to answer this question. Purposive sampling targets Kenyan military officers at various levels, representatives of the state, institutions and organizations working directly with the Kenyan military and representatives of civil societies and members of communities impacted by the presence of military troops in their locality. Face-to-face interviews and focus group discussions will inform data generation through semi-structured interviews. Concepts in doctrines influencing civil-military relations, the role of the military in counter-terrorism and foreign military support in Kenya are the basis of the conceptual framework. Theories on new wars by Kaldor, 1999 and Rebecca Schiff, 2009 concordance theory on civil-military relations will form part of the literature review. Thematic data analysis will be applied to the large amount of data generated to highlight significant statements and generate meaning units from which an essence description will be developed.