Part 2 – Why We Struggle to Think Clearly: When the Higher Brain Gets Hijacked

The Brain and Regulation Trilogy

In Part 1 – The Alarm System, we explored the lower brain: the part that drives anxiety, fear, and other instinctive reactions. This next step looks at the other half of the story – the higher brain – and why we lose access to clear, flexible thinking when the body’s alarm is on.

The higher brain sits at the top and front of our head, mostly in the prefrontal cortex. It’s the part that allows us to think, plan, imagine, use language, and hold complexity. It can imagine a future that doesn’t yet exist, reflect on the past, and hold several ideas or emotions at once. This is also the part that can look at ourselves from another perspective. It lets us notice: I’m angry right now, or I’m scared but I can still choose what to do. That self-observation – what neuroscience calls metacognition – is uniquely human. It’s what allows reflection, empathy, and conscious choice.

Most of what we call thinking in everyday life happens here, and it’s the part of the brain our modern world depends on: making plans, writing, communicating, raising children, solving problems, managing complex emotional regulation. Almost everything that matters to our functioning as people and societies comes from this higher system.

The difficulty is that when the alarm system is activated in danger mode, the higher brain can’t work at its best. The stress response diverts energy toward the body and emotional centres. The prefrontal cortex – which needs calm and oxygen to think clearly – goes partially offline. So even though we might still be trying to think, the thinking becomes narrow, rigid, and fast paced. It turns into survival thinking: thought focused on quick solutions and control. It loses its ability to hold complexity and nuance, to see context, or to consider more than one perspective. This is the opposite of safe thinking, which happens when the brain is regulated and can integrate feeling, reason, and meaning at the same time.

We see this in everyday life: forgetting what we meant to say in an argument, replaying a conversation to fix it, lying awake rehearsing what could go wrong. The higher brain is still trying to make sense of what happened, but it’s under the influence of the alarm. The result is a loop of anxious thinking – what research calls rumination or perseverative cognition – where we feel active but are really just recycling the threat.

The more the alarm system stays active, the less clearly we can think. The higher brain doesn’t disappear – it just loses its full range. Language becomes limited, imagination turns into prediction, and planning becomes control. That’s why we can’t reason or count to ten our way out of distress: the very system that does reasoning is being overruled. This isn’t a failure of willpower or intelligence. It’s how the brain was built – an ancient engine running a modern machine. The higher system needs safety to operate. Without it, the mind becomes busy but not effective, clever but not wise.

When the nervous system’s alarm stays switched on, the higher brain can’t do what it’s meant to do: think clearly, feel connected, and hold perspective. In Part 3 – What Actually Regulates, we’ll explore how to bring the brain back to safety – what truly helps the higher system come online again, so thought, emotion, and action can work together.