Why You Have 3 Brains, Not One

We talk about the brain like it’s a unified decision-maker, but that’s far from the reality—especially in clinical work. I’ve found again and again that when people struggle with internal conflict, emotional dysregulation, or impulsivity, it’s not that their brain is malfunctioning. It’s that multiple parts of the brain are doing exactly what they were built to do—but they’re working in parallel, not in sync.

This is where the triune brain model still holds conceptual value, even if it’s not a perfect anatomical map. It gives us a shorthand to talk about how deeply layered human behavior is. We’ve got an ancient survival engine, an emotional translator, and a forward-planning storyteller—and they’re often not on the same page.

So in this post, I want to explore how those systems interact under stress, why they so often clash, and what it means for the work we do as therapists, coaches, or mental health professionals.

The three brains doing their own thing

Let’s dive into the triune model—not just what it is, but why it still matters when you’re sitting across from a client who’s spiraling, shutting down, or lashing out.

The survival brain: Not subtle, but very fast

This is the oldest part—the reptilian brain, mainly the brainstem and basal ganglia. It doesn’t “think” in the way we define thought. It just reacts. Heart rate, breath, reflexes, core drives like hunger, aggression, and territoriality—it’s all here.

This part of the brain is lightning-fast and almost impossible to override in real time. And in a survival context, that’s great. You don’t want to analyze a lion’s facial expression before running. But in therapy, this shows up as panic attacks, shutdowns, rage, compulsions. And clients don’t know why it’s happening.

Example: A client in couples therapy might storm out of the room during conflict. They later say, “I don’t know what came over me.” Well, they didn’t walk out. Their survival brain did. It perceived threat (not being heard, being criticized), and hijacked motor control.

So when we’re trying to “talk someone down” using logic, we’re appealing to the wrong brain. The survival system has already pulled the emergency brake.

The emotional brain: The storyteller of danger

Next is the limbic system, which includes the amygdala, hippocampus, hypothalamus, and more. This is where emotional memory lives. It’s pattern-driven. If the brainstem screams “threat,” the limbic system interprets: What kind of threat? Is this like last time? Should I be angry or ashamed?

This is where trauma gets sticky. The limbic system doesn’t care much about time—it cares about pattern similarity. So if someone yells at you now the way your father did when you were six, the limbic system might fire up the same emotional response. Rationally, you know it’s your boss, not your dad. But emotionally, it’s déjà vu all over again.

And here’s the kicker: the limbic system can amplify the signals from the survival brain. A racing heart makes the amygdala go, “Oh no—danger!” even if the original stimulus was just mild stress.

This is also where attachment gets wired. When a client feels abandoned, triggered, or chronically unseen, it’s the limbic system that responds first—often long before they can explain what they’re feeling.

The rational brain: Slow, smart, and easily shut down

Finally, we’ve got the neocortex, especially the prefrontal cortex. This is the part we often wish ran the show. Language, abstract reasoning, problem-solving, inhibition, empathy—all here.

When it’s online, we can reflect, negotiate, and choose wisely. But it’s energy-intensive, and it’s the first to go offline under stress. That’s not metaphorical—it’s backed by research in neuroimaging and stress physiology. Cortisol and norepinephrine dampen prefrontal activity, favoring older, faster systems.

Example: A teenager in a high-pressure exam might “blank out” completely. Their cortex goes dark. The reptilian brain floods the system with stress signals; the limbic system adds anxiety and fear of failure. Boom—no working memory, no language access.

This also explains why cognitive approaches (like CBT) often don’t land when someone is activated. The cortex isn’t leading at that moment. It’s in the back seat, hands off the wheel.

How these systems collide (and confuse clients)

Let’s be real—clients don’t experience “three brains.” They just feel torn, stuck, overwhelmed, or ashamed. But when we understand these systems, those feelings make sense.

A person who grew up in chaos might react to calm relationships with distrust. Their limbic system says, This feels unfamiliar, maybe unsafe.
Someone might understand they’re safe now, but still freeze when touched. Their survival brain says, Touch equals danger, and the cortex can’t override it.
A client might say they want to forgive someone but keep replaying past pain. That’s limbic encoding—emotionally, the story hasn’t resolved.

Understanding this model helps us hold compassion for these disconnections. It also gives us a map for sequencing interventions. We can start with bottom-up regulation (breath, grounding, movement), then layer in relational safety (limbic soothing), and only then ask for cognitive reflection.

It’s not that any of the three are “wrong.” They’re just running different operating systems. The work is in integration, not dominance. And that starts with knowing who’s in charge in any given moment—and why.

How the three brains show up in daily conflict

Let’s make this practical. Because if you’ve ever sat with a client mid-meltdown—or had your own—you know this isn’t just theory. These three systems fight for control all the time, and it plays out in some deeply familiar ways. What makes the triune brain model useful isn’t how neatly it divides anatomy, but how powerfully it maps internal conflict.

When we understand that conflict, we can guide people toward integration rather than reactivity.

Here are a few real-world situations where the three brains crash into each other—and how to recognize who’s steering the ship in each case.

Relationship fights that escalate fast

Client example: Let’s say someone is in a heated argument with their partner. It starts with “Why didn’t you text me back?” and ends with shouting, door-slamming, and silence for hours.

Reptilian brain jumps in first: It hears criticism as danger and goes straight to fight-or-flight. Elevated heart rate, clenched jaw, pacing the room—that’s pure survival mode.
Limbic brain adds emotional fuel: Maybe the person felt abandoned as a child. That unreturned text now feels like abandonment. The emotional brain doesn’t care if the logic holds; it cares that the pattern matches.
Neocortex is barely online: The person can’t articulate why they’re upset. They’re flooded. Rational thought, empathy, and memory of their partner’s good intentions are MIA.

Even couples with strong attachment can get stuck in this loop. And telling someone to “just calm down” or “be reasonable” is like shouting at a locked door. You’re talking to the cortex, but the cortex left the building five minutes ago.

Public speaking panic

Client example: A high-functioning executive is confident in meetings but melts down before presenting to a large crowd.

Reptilian brain reads the spotlight as a predator’s gaze. The body tenses. Breathing becomes shallow. Eyes dart.
Limbic system activates past shame: Maybe they got laughed at in school once. The emotion returns, full-force.
Neocortex fails to access rehearsed content. They blank out on stage—not because they’re unprepared, but because their logical brain is outmatched by their emotional and survival systems.

We often treat public speaking anxiety as a skill deficit, but this model reframes it as a threat mismatch. The solution isn’t just practice—it’s nervous system regulation.

Decision paralysis

Client example: A young adult stuck in a career dilemma can’t choose between two seemingly equal options. They research obsessively, ask for input, but stay frozen.

Reptilian brain resists change: It hates the unknown. No movement feels safer than risking danger.
Limbic brain cycles through fear of regret, fear of judgment, fear of failure. The emotional brain spins without resolution.
Neocortex is trying—but overloaded. It creates pros and cons lists, but analysis turns into anxiety.

The result is a stuck loop, not because the person is indecisive, but because three systems are pulling in different directions.

Trauma responses that confuse logic

Client example: A survivor of early relational trauma finds herself repeatedly entering relationships with emotionally unavailable partners—and doesn’t understand why.

Reptilian brain is drawn to familiar nervous system states—chaotic, tense, unpredictable.
Limbic system wires in attachment templates early. To it, pain equals love.
Neocortex might say, “I know this isn’t good for me.” But knowledge alone isn’t enough to override the pattern.

This is where therapists get stuck trying to offer insight, when what the system really needs is bottom-up healing and relational re-patterning.

When we understand the dynamic between these three systems, we stop blaming clients for “sabotaging” themselves. We can see it for what it is: a tug-of-war between parts that are all trying to help—but with different tools and outdated instructions.

Tools to bring the three brains into alignment

Now that we’ve seen how the three-brain tug-of-war plays out in real life, let’s talk about how to help. Because here’s the truth: integration isn’t something that happens automatically—it’s built, slowly, with practice.

And depending on which brain is dominating, you need a different kind of entry point. I like to think of it as working from bottom-up, middle-out, or top-down.

Bottom-up: Calming the survival brain

You can’t reason with a nervous system that’s in a red-alert state. That’s why bottom-up approaches go through the body first.

Breathwork

Slowing the exhale engages the parasympathetic nervous system—especially the vagus nerve. When someone is stuck in fight-or-flight, you can often get more traction with five minutes of paced breathing than twenty minutes of talking.

Somatic grounding

Tools like orienting (noticing objects in the room), pressing feet into the floor, or using cold temperature shifts can pull someone out of a survival loop. This is especially helpful for dissociation and freeze responses.

Movement

Shaking, stretching, or even walking can discharge built-up energy. Trauma lives in the body, and unless we create exit routes for that energy, the reptilian brain stays on high alert.

Polyvagal-informed work

Understanding dorsal (shutdown), sympathetic (fight/flight), and ventral (safe/social) states can help clients track their responses and build nervous system literacy.

Middle-out: Engaging the emotional brain

Once the survival brain is calmer, the emotional system becomes the next access point. This is where therapy often starts feeling personal and healing—not just regulated.

Affective labeling

Dan Siegel’s “name it to tame it” works because labeling an emotion engages the prefrontal cortex, which can help quiet the amygdala. It’s simple, but powerful. “I feel ashamed” is a neural intervention, not just a sentence.

Inner parts work (like IFS)

IFS is especially good for working with limbic patterns. By helping clients identify “parts” that hold pain, fear, or protectiveness, we’re creating enough space for the cortex to witness the limbic content without getting flooded.

Relational resourcing

Because limbic pain is usually encoded through relationship, it often needs relationship to heal. That can be through co-regulation with a therapist, repair conversations, or even rescripting memories.

Top-down: Using the thinking brain wisely

This is where CBT, narrative therapy, and mindfulness come in—but only when the system is ready.

Cognitive reframing

If a client is regulated enough, challenging distorted beliefs can create new neural pathways. But if they’re still in a limbic or reptilian state, you’ll just trigger resistance.

Mindfulness

Mindfulness strengthens the prefrontal cortex’s ability to observe without reacting. Over time, this builds what some call “cortical override”—the ability to notice a trigger and choose a different response.

Mentalization

Teaching clients to reflect on their own mental states and others’ intentions (especially in attachment work) is a deeply cortical process. It rewires how we interpret conflict and reduces reactive loops.

What matters is not just what you use, but when. Sequence is everything. The mistake I often see in high-functioning clients is they want to “think” their way out of a dysregulated state. But if you haven’t built bottom-up safety and middle-out connection, top-down tools will slide off the surface.

And integration doesn’t mean silencing any part. It means each brain gets to do its job in balance—protection, connection, and reflection, all working together.

Final Thoughts

The triune brain model may be imperfect, but it gives us something incredibly valuable: a map for understanding internal conflict as a systems problem, not a character flaw.

We’re not irrational. We’re running multiple intelligent processes with different priorities. The survival brain wants to keep us alive. The emotional brain wants to protect our story. The thinking brain wants to make sense of it all. When those systems stop competing and start collaborating, that’s when we see real healing—not just symptom relief, but transformation.

And that’s the work—helping people build enough internal safety that they don’t just survive, or feel, or think, but integrate all three.