The more I learn, the harder it is to answer, because there are so many pieces involved. Also the biology of methylation cycle work is very new science, and various experts have strong opinions and agenda.
Also, of course, on these forums, those of us who have been sick a long time are understandably touchy about the very hard work we've already done to make what progress we have made. Whatever system, prescriptions, supplements, experts, or doctors we are using to get better, we want them to be right, and the risks of making a mistake can have serious consequences if our illness resumes. Defensiveness is perfectly understandable -- indeed, we each have an obligation to ourselves to be defensive of our health, and that means of our approaches to finding it. Really, all I can say for sure is that this protocol works for me.
This is a good place to link to my general disclaimer and my Oct 2014 summary of my deep-end ramp-up. Please note that my supplementation has changed in the time since Oct 2014, most importantly lowering my B1,B2,B3.
So, what is the Methylation Cycle?
Here's how I understand it: methylation is a biochemical process that happens in the body's cells, billions of times every second. It affects a wide range of biochemical functions, including: the immune system, inflammation, handling toxins, creation and synthesis of neurotransmitters (dopamine, serotonin, GABA, etc) that are critical to sleep, cognitive function, and memory. It therefore provably or likely affects a number of conditions, such as heart disease, diabetes, cancer, autism, CFS, Alzheimer's', pregnancy problems, allergies, digestion, various mood disorders, and other and various aging effects. The methylation cycle is affected by, among other things, genetic variations, disease, environmental toxins, aging, and physiological trauma.
What is the Freddd Protocol?
Freddd himself does not call this his "Protocol" -- that tag has been given by those of us following in his footsteps, as a shorthand to "You know that stuff that Freddd has been doing that he credits with saving his life? I'm doing that, too."
Freddd's work is best conveyed in his words, even though they are not always easy to piece through, especially if you're already suffering from brain-fog brought on by partially blocked methylation (oh, the irony). If you want a simpler, digested version, see below.
To get started on Freddd's overview of all this, in his own words, I'll direct you to his Feb 2013 post: The Stages of Methylation and Healing. While some things have changed since then, much of this remains the heart of what the rest of us call the Freddd Protocol.
Some Shorter, Digested Guides for the Freddd Protocol:
@ahmo's guide: A Guide to Freddd's Protocol
@sheclimber start-up notes: My understanding of Freddd's Protocol