I think your question highlights some of the difficulties in making sense of human behaviours. There is no doubt that the brain is the center of executive decision making and behaviour, it also provides many of the functions that inform these aspects of mind. It also provides a host of functions essential to maintaining homeostasis and maintaining our safety, these often operate outside of awareness and tend to be easier to link to our biology.
If we use your example of fear responses and try to map how the processing works, we have a number of sensory systems that provide us with information about our environment, unfortunately we don't have the cognitive capacity to process everything we are exposed to. So evolution has provided us certain rules, that appear built in, the help us prioritize what we attend to and how. Obviously indicators of danger are important but we can't really have automatic rules for all situations so it seems we react to stimuli that are sudden, unexpected, and intense, these being modified by isolation, darkness and movement. So when someone jumps out behind, when your not expecting it and making a loud noise, these automatic systems are immediately activated, its very fast there is no thinking involved and it activates a limited set of reactions – fight, flight or freeze. Similar things are seen in many animals.
Its usually the amygdala that is identified in initiating these reactions and it initiates a massive physiological set of adaptations to help cope with danger. At the same time, the amygdala is using its extensive networks of connections so that more elaborate and detailed processing of the threat is made, using prior experiences and reasoning, though this will still be biased by the emotions. We always overestimate threat, because its safer to do so but it is at the level of the amygdala that the results of this processing is used to modify the physiological responses. The amygdala is involved in all emotional processing and also helps attach emotional value to memories, working with the hippocampus. Memory storage occurs throughout the brain apparently organised by systems of association with other memories and with the sensory systems, it also appears to be highly redundant.
So in this we can identify an area that is clearly involved near the start of a process, but it then activates a number of other networks, which in turn activate others. An example might be in the fact that conscious processing usually involves language, so those processes will be activated. Emotion is also seen as a major motivator so there are behavioural systems involved.
What neuroscientists are faced with when they scan the brain is an organ involved in a huge number of tasks all the time and which appears to be very flexible in the way it routes information around. Its always active and they have to use computers to analyse the mass of data they are presented with in order to identify networks of activity that can be linked to specific states. Its no easy task.
However we look at things its likely that how we interact with our environment will be represented by changes in the brain, this will usually not be a straight forward cause and effect relationship.
I think its unlikely that there is anyone specific point of entry, information is fed into the brain through a variety of sensory systems and of course the brain itself, from previous experiences can be the source of intense effects. The cingulate gyrus forms part of the cingulate cortex and is quite a large area which seems to act as an interface between the more automatic emotional areas and the cortex. Again it is involved in multiple functions is highly interconnected and has been an area of interest in mental health.
Its true that in many cases depression is characterized by lower levels of activity both in behaviour and in cognition but none of this has really helped us to understand suicide which may have a number of motives. We know being suicidal is not usually a consistent state, often involves the loss of hope (its often about the future not the past) and frequently involves the use of dis-inhibiting drugs.
Sorry its a long answer.