The Short Answer
The Scorch Protocol's standard sequence is dry fasting → T3 therapy → refeeding plus hGH → rotation. For most chronic illness patients, this sequence is the right entry point. For specific patient profiles, the sequence is modified: severely depleted patients with very low basal body temperature start with T3 first; very mildly affected patients may not need the full protocol; patients with active acute infections need to address those first. The decision tree below walks through the entry points based on your specific profile and the signals that point to each path.
The Baseline Tracking Required Before Any Decision
Before deciding which protocol entry point fits your situation, you need baseline data. The minimum:
Two weeks of daily basal body temperature tracking. Oral, taken before getting out of bed in the morning, before any movement or speech. Average the readings. This is the single most important data point for protocol decisions; it is the functional readout of your cellular metabolic state and is the only objective marker that drives the major protocol sequencing decisions.
Two weeks of resting heart rate tracking. Morning, before getting out of bed. Establishes the cardiovascular baseline.
Symptom inventory. A current list of your symptoms, their severity, what triggers them, what helps them. This is what defines your starting point and what you will be tracking against during the protocol.
Illness duration estimate. Roughly how long have your current symptoms been ongoing. This is one of the variables in the decision tree.
Current medications and supplements. Some medications affect protocol sequencing; certain medications are contraindicated during specific phases.
If you have access to labs, baseline labs (TSH, free T4, free T3, reverse T3 if available, morning cortisol, CBC, comprehensive metabolic panel, ferritin, vitamin D, vitamin B12) are useful but not required. The protocol is designed for self-administration without lab access; the temperature data is the primary objective marker.
Decision Point 1: Are You Currently in Acute Illness?
Before any chronic illness protocol decisions, the acute layer needs to be addressed:
- Active confirmed Borrelia infection. Address with appropriate antibiotic treatment first; the Scorch Protocol is for after the acute layer has been addressed.
- Active SARS-CoV-2 infection. Wait for the acute infection to clear and the immediate post-acute window (typically 8-12 weeks) to elapse before starting the chronic protocol.
- Active fungal infection requiring antifungal therapy. Address the acute layer first; the protocol can begin once the acute treatment is complete.
- Recent surgery or major medical event (less than 12 weeks ago). Complete the recovery from the acute event before starting the protocol.
If any of these apply, complete the acute treatment first. The protocol pages and the chronic illness recovery guides are still useful reading during this window for understanding what comes next.
Decision Point 2: What Is Your Basal Body Temperature?
This is the single most important branch point in the decision tree.
Path A: Basal temperature 97.5°F or higher
This is the relatively rare profile for a chronic illness patient seeking the Scorch Protocol; it means your metabolic floor has not significantly dropped. The protocol may still be appropriate but the entry sequence is unmodified.
Standard entry: Preparation → first dry fast → T3 if needed → refeeding plus hGH if appropriate.
The right entry point in this profile is the protocol overview in the Long Covid Recovery guide or the chronic illness guide most matching your symptom profile.
Path B: Basal temperature 96-97.4°F
This is the most common profile for the Scorch Protocol's target chronic illness population. The metabolic floor has dropped meaningfully but not into the lost-cause range. The standard protocol sequence applies.
Standard entry: Preparation → first dry fast → T3 → refeeding plus hGH → rotation.
The right entry point is the chronic illness guide most matching your symptom profile, then the preparation page, then the dry fasting complete guide.
Path C: Basal temperature 95-95.9°F
This is the "borderline" cohort. The metabolic floor has dropped substantially. Most patients in this range will benefit from T3 first to raise the foundation before attempting extended fasting.
Modified entry: Preparation → T3 therapy first → short fast tolerance building → standard sequence once temperature stabilizes above 96°F.
The right entry point is the T3 therapy complete guide and the chronic illness guide most matching your symptom profile.
Path D: Basal temperature below 95°F
This is the "over-adapted" or "lost-cause fasting" profile. The metabolic floor has dropped into territory where attempting an extended fast at the current baseline is more likely to produce symptoms than therapeutic benefit. T3 therapy first is mandatory; the protocol sequence is meaningfully modified.
Modified entry: Extended preparation → T3 therapy first → very gradual tolerance building → first 5-day fast only after temperature stabilizes above 96°F.
The right entry point is the 5-year ME/CFS protocol walkthrough which covers this modified sequence in detail, and the T3 therapy complete guide.
Decision Point 3: What Is Your Illness Duration?
After the temperature decision, illness duration shapes the rest of the path.
Less than 1 year
Shorter illness duration is associated with faster and more complete recovery. A 5-day dry fast plus one T3 cycle frequently completes recovery for this cohort if the basal temperature is above 96°F and no significant co-infections are involved.
The right entry point is the chronic illness guide most matching your symptom profile, then the dry fasting complete guide. Plan for a shorter protocol arc; you may not need the full rebuild phase.
1-5 years
The middle range. The standard protocol arc applies: multiple T3 cycles, hGH layering during rebuild, 9-18 month timeline for substantial recovery.
The right entry point is the chronic illness guide most matching your symptom profile, then the standard protocol sequence.
5-10 years
The longer-duration cohort. Multiple dry fast cycles often required, often including 7-day or 9-day fasts after building tolerance. The rebuild phase is longer; hGH cycles may need to be longer or more frequent.
The right entry point is the ME/CFS Recovery guide (the framing best matches long-duration cases), the 5-year ME/CFS protocol walkthrough, and the standard protocol sequence with extended timeline expectations.
10+ years
The longest-duration cohort. The rebuild is possible but takes 2-3+ years. Structural neurological adjuncts (psilocybin neuroplasticity) often become relevant for residual cognitive symptoms.
The right entry point is the ME/CFS Recovery guide and the extended-timeline framing throughout. The protocol works; the timeline scales with duration.
Decision Point 4: Which Specific Conditions Are Layered On Top?
The chronic illness baseline is the underlying mechanism. Specific layered conditions require modifications:
MCAS active and significant
Modified refeed schedule (slower than default), MCAS medication continuity through the protocol, MCAS-aware food choices during refeed. See Long Covid and MCAS for the implementation details.
POTS active and significant
Continued POTS medications through early protocol, planning for orthostatic intolerance during fasts, salt loading taper during rebuild. See POTS After Covid for the implementation details.
Significant brain fog as dominant symptom
T3 therapy typically produces the most direct relief for brain fog; the cellular metabolic restoration is what reopens cognitive function. See Long Covid Brain Fog for the mechanism and protocol-specific implementation.
Chronic Lyme background
Address acute infection markers if present; complete any active antibiotic course before starting the protocol; co-infection treatment fits into the rebuild phase. See the chronic Lyme recovery guide.
Long-term carnivore or strict keto background
The carbohydrate transition is uncomfortable and often produces frightening liver pain that is not damage. See Carnivore to High-Carb Transition for the management.
Decision Point 5: Do You Have Absolute Contraindications?
Some conditions are absolute contraindications to the protocol or to specific phases:
Absolute contraindications to dry fasting: pregnancy, breastfeeding, type 1 diabetes, severe kidney disease, severe heart disease, active eating disorder, active GI bleeding. See Is Dry Fasting Safe? for the full list and the relative contraindications.
Absolute contraindications to hGH therapy: active malignancy, recent cancer history, certain pituitary conditions, severe diabetic retinopathy.
Conditions requiring specialized medical input: type 2 diabetes (medication adjustment), pre-existing liver disease (baseline monitoring), severe psychiatric conditions (separate clinical support).
If any of these apply, the protocol may still be partially appropriate (different phases may still be available) but the planning needs specialized clinical input.
What If Multiple Paths Seem to Apply?
The decision tree is hierarchical: temperature is the strongest signal, then illness duration, then layered conditions, then contraindications. If your situation has features pointing to multiple paths, the higher-priority signal generally wins.
For example: a 3-year Long Covid patient with basal temperature 94.5°F and active MCAS would be:
- Temperature 94.5°F → Path D (T3 first, modified sequence)
- Illness duration 3 years → standard protocol arc
- Active MCAS → MCAS-specific refeed modifications
- No absolute contraindications
The right entry: the 5-year ME/CFS protocol walkthrough (the modified sequence framework applies even though the illness duration is shorter), plus Long Covid and MCAS for the MCAS-specific implementation, plus the T3 therapy complete guide for the entry-phase execution.
What If None of the Paths Seem to Apply?
A few specific situations where the standard decision tree may not fit:
You have chronic symptoms but no clear chronic illness diagnosis. The protocol applies to the underlying metabolic mechanism regardless of which formal diagnosis your symptoms have received. If your basal temperature is below 97.5°F, you have symptoms consistent with metabolic collapse (fatigue, brain fog, temperature dysregulation, food sensitivities, exercise intolerance), and standard care has not produced sustained improvement, the protocol may be appropriate.
Your symptoms do not match the Long Covid, ME/CFS, or chronic Lyme profile. The protocol is mechanism-based, not diagnosis-based. The Scorch Protocol mechanism applies to metabolic collapse from any upstream cause. If the mechanism fits, the protocol applies regardless of the specific etiology.
You are unsure if you are sick enough to need this protocol. The protocol is calibrated for chronic illness; it is not a wellness experiment for healthy people. If you are not sure you need it, you probably do not; less intensive interventions are appropriate first.
You have multiple complex conditions that do not fit any of the standard paths. This is the situation where individualized clinical input from someone experienced with the protocol is most useful. The decision tree is a starting point, not a substitute for clinical judgment in complex cases.
Frequently Asked Questions
Should I do this protocol with a doctor?
Ideally, yes, particularly for the T3, hGH, and antimicrobial layering components. The reality is that most physicians are not familiar with the protocol; telehealth services experienced with the protocol exist. The list of pharmacies page is a starting point for finding experienced practitioners.
How long before I see results?
For Path A and B patients with shorter illness duration, initial improvement often appears in weeks 1-4 of the protocol. For Path C and D patients, the modified T3-first sequence produces initial improvement in months 2-4 as the foundation is being built. Substantial recovery is typically 6-12 months for the standard cohort and 12-24 months for the long-duration cohort.
What if I am wrong about my baseline temperature?
This is why the two-week tracking is required. A single low reading or a single high reading is not enough; the average over 14 days is what drives the decision. If you have not done the tracking, do it before making protocol decisions.
Can I do this protocol myself?
The dry fasting and refeeding phases can be self-administered with proper preparation. The T3, hGH, and prescription antimicrobial phases require prescribing physicians. The full self-administered protocol is feasible for moderately ill, motivated patients; severely ill patients should have at minimum a buddy system and prescribing physician involvement.
Where do I start reading?
Match your profile to one of the chronic illness recovery guides:
- Long Covid Recovery guide for post-Covid presentations
- ME/CFS Recovery guide for pre-COVID-onset CFS/ME presentations
- chronic Lyme recovery guide for Lyme-background presentations
Then move into the dry fasting complete guide and the T3 therapy complete guide for the mechanism context, and the relevant protocol pages for practical execution.
Where to Start
Match your basal body temperature, illness duration, and layered conditions to the decision points above. The right entry point depends on your specific profile. The protocol is mechanism-based and modular; the sequencing flexibility exists specifically because patients vary substantially in their starting point.
For the standard cohort (basal temperature 96-97.4°F, illness duration 1-5 years), the entry is the chronic illness recovery guide matching your profile, then the standard sequence. For the modified-sequence cohorts (basal temperature below 96°F, long-duration cases), the 5-year ME/CFS protocol walkthrough and the T3 therapy complete guide are the entry points.
Read Should I Start with Dry Fasting or T3 Therapy First? for the most common sequencing question in detail.
Related Protocol Section
This article explains the science behind a specific phase of the Scorch Protocol.
Read the full protocol section →