01 of 07
Read this in order
This is the framework Jimmy used to put ulcerative pancolitis into remission twice, and clear H. pylori, candida, SIBO and dysbiosis along the way.
Everything here is sequenced on purpose. The sequence matters as much as the phases.
| Phase | Focus | Keyword |
|---|
| Phase 1 | Pull inflammation, reset the nervous system, test food reactivity | FIRE |
| Phase 2 | Seal and repair the gut lining | SEAL |
| Phase 3 | The kill phase | KILL |
| Phase 4 | Mitochondrial rebuild | ENERGY |
| Phase 5 | Reseed the microbiome | SEED |
Who this is for
- Autoimmune, UC, Crohn’s or chronic gut issues you are managing alongside a physician.
- Exhausted, bloated, not responding to training despite doing everything right.
- Protocols that made you feel worse rather than better.
- A plateau no program change has fixed.
02 of 07
Phase 1 · Pull the inflammation
The step nobody does for long enough
The body cannot heal in an inflamed state. Before any protocol, supplement or kill phase, the fire has to come down.
Inflammation and nervous system dysregulation feed each other. Break that loop and everything downstream becomes possible. Three pillars run at the same time, not one after the other.
01 · Anti-inflammatory nutrition
A Mediterranean shaped foundation. Wild caught fish, olive oil, dark leafy greens, dark berries, turmeric, ginger. Processed food, refined sugar, seed oils and alcohol come out. You are not chasing calories or macros here, you are chasing food quality and lower reactivity.
02 · Food sensitivity testing
An MRT run during this phase, not after it. It measures the immune system’s inflammatory response to specific foods and gives a personalised reactivity map. Elimination diets built from a generic list are guesswork by comparison. Foods come back in as symptoms settle.
03 · Nervous system regulation
Morning sunlight for circadian rhythm and the cortisol awakening response. Daily cold exposure for vagal tone. Breathwork for CO2 tolerance and autonomic state. Humming, which vibrates the vagus nerve directly and costs nothing. Ten minutes of meditation daily moves HRV measurably.
The pointYou cannot out-supplement a nervous system stuck in fight or flight. The gut and the brain are on the same line, so both get addressed together.
TimelineTwo to four weeks minimum before Phase 2. You are ready when symptoms are reducing and energy is stabilising. Every phase after this one depends on this one.
03 of 07
Phase 2 · Seal and repair the lining
The step that changes everything downstream
A leaky gut during a kill phase makes everything worse. Repair the wall before going after what is damaging it.
The intestinal wall is one cell thick. Tight junctions hold those cells together and keep bacteria and toxins on the correct side of it. Pathogens, inflammation and stress prise those junctions open, and once they are open, bacteria, toxins and undigested food reach the bloodstream. The immune system attacks them. That is where the systemic inflammation, the autoimmune flares, the brain fog and the hormonal disruption come from.
| Mechanism | What it does |
|---|
| Mucosal support | Soothes and coats the intestinal wall and brings surface inflammation down before deeper repair starts. |
| Tight junction integrity | Targets the junctions themselves. This is the difference between soothing a gut and actually sealing one. |
| Tissue repair | Active support for the structural damage pathogens leave behind. Peptide therapy has shown real clinical promise for GI tract regeneration. |
| Immune modulation | In autoimmune conditions the immune system attacks the lining itself. Repair fails while that continues. |
TimelineFour to six weeks, with Phase 1 still running underneath it. Do not abandon Phase 1 here. Move on when symptoms have meaningfully reduced.
04 of 07
Phase 3 · The kill phase
Why most gut protocols fail here
Pathogens are survivalists. They build protective biofilm, adapt to a single antimicrobial, and thrive in an inflamed environment.
Why people feel worse
- They skipped Phases 1 and 2. The environment is still inflamed and drainage is still shut.
- They went straight to antimicrobials. No biofilm disruption first.
- They used one antimicrobial continuously. The pathogens adapted.
- They kept training hard. Healing resources got split.
- They had no GI Map. They were guessing at the target.
The four steps, in order
| Step | Why it sits here |
|---|
| Biofilm disruption | Antimicrobials cannot penetrate the coating pathogens build around themselves. Skip this and you are throwing compounds at a wall. This is the step most protocols miss entirely. |
| Targeted rotation | Antimicrobials chosen from what the GI Map actually found, and rotated, because pathogens adapt to a single compound over time. |
| Die off management | Dying pathogens release toxins. Fatigue, fog, skin changes and gut discomfort can spike. Drainage and liver support reduce how hard that lands. |
| Training pullback | Three days a week at RPE 7. The body is already running one war. Body composition often improves here anyway, despite the lower volume. |
Test before this phaseGI Map to identify what is present and at what load. Bloodwork for liver, inflammatory and immune markers. Retest after with a follow up GI Map rather than assuming clearance.
TimelineFour to eight weeks depending on pathogen load.
05 of 07
Phase 4 · Mitochondrial rebuild
Why you are still exhausted after the kill phase
Chronic inflammation, active infection and gut damage wreck mitochondrial function. When the energy factories are compromised, no amount of sleep or clean eating fixes the exhaustion, because the problem is cellular.
What damaged mitochondria look like
Persistent fatigue regardless of sleep. Poor exercise tolerance and slow recovery. Brain fog. Body composition stalling on clean nutrition. Hormonal dysregulation. Low HRV and poor stress resilience.
| Layer | The job |
|---|
| Support what exists | Give existing mitochondria the raw material to run the electron transport chain properly. The active forms of those compounds matter here, not all forms are equal. |
| Build new ones | Mitochondrial biogenesis. This is how capacity gets rebuilt rather than just maintained. |
| Clear the damaged | Mitophagy. Damaged mitochondria generate oxidative stress and drag the whole system down. Take the rubbish out before restocking. |
| Cut oxidative stress | Specifically at the inner membrane, where the most damaging free radical production happens. |
What amplifies itZone 2 cardio is the strongest mitochondrial training stimulus there is. Cold exposure carries over from Phase 1. Morning sunlight and red light support energy production. Most mitochondrial repair happens in deep sleep, and chronic cortisol undoes it.
TimelineEight to twelve weeks minimum, running alongside Phase 5. Energy, HRV, training output and body composition are the markers.
06 of 07
Phase 5 · Reseed the microbiome
The step that decides whether you stay healed
Clearing pathogens creates space, and space gets filled by whatever is available. Reseed deliberately or the wrong things come back.
What people get wrong
Taking a generic probiotic after a kill phase is guessing, not reseeding. Most supplements do not survive the gastric environment to reach the colon. Strain specificity decides what actually happens. And organisms arriving into an environment that cannot sustain them do not colonise.
| Keystone species | Why it decides the outcome |
|---|
| Akkermansia muciniphila | Lives in the mucus layer and protects the lining directly. Regulates the same tight junctions Phase 2 repaired. Tied to insulin sensitivity and body composition. Low levels track with metabolic dysfunction and autoimmune flares, and standard probiotics do not replace it. |
| Butyrate producers | Butyrate is the primary fuel for colon cells. Without it the lining starves and inflammation climbs. They also do a large share of immune regulation inside the gut. |
How reseeding runs
- The environment comes first. Phases 1 to 4 are what make colonisation possible at all.
- Feed it with food the gut can handle at that point, guided by where testing says the gut actually is rather than a generic list.
- Introduce targeted strains based on what the GI Map showed was depleted.
- Verify at twelve weeks with a follow up GI Map, to confirm the keystone species came back.
Why this phase existsJimmy finished his first full protocol without fully restoring these two species and relapsed a year later. That is the reason this phase is written out rather than assumed.
07 of 07
The bottom line
These five phases work because they run in sequence. Each one builds the conditions the next one needs.
Skip a phase or rush it and the protocol fails, and it fails on order rather than on approach. That is the single most common reason someone arrives having already tried most of what is in this guide.
The recomposition that follows is not something you chase. It is what a body does once it is no longer fighting itself.
The mechanism behind that is the subject of the companion guide, The Recomp Framework. The three phase version of this same sequence is in The R3 System.
Educational contentThis guide is educational and is not medical advice, diagnosis or treatment. Coaching runs alongside your physician, not instead of them. Individual results vary. Always speak to your healthcare provider before starting a new protocol or supplement, especially if you have a medical condition, are pregnant or breastfeeding, or take medication.