Do the adrenal glands get addressed at any point of the protocol? When the methylation improves, do the adrenal glands get better as a result? Do you recommend some plants or other stuff for adrenal gland fatigue?

No, so, adrenal fatigue isn't real. Your adrenals don't get fatigued. That’s a myth.  

But that doesn’t mean that the symptoms of "adrenal fatigue" aren't real. They’re definitely real. 
So, brain fog, low energy, depression. These are all symptoms of “adrenal fatigue”, right? And these symptoms are definitely real. But they’re not caused by your adrenals being fatigued.  
So, a lot of practitioners will diagnose adrenal fatigue. But they don’t dig deep enough.  
There are two actual causes of “adrenal fatigue”.  
Number one is mitochondrial dysfunction. And the entire program addresses that. Your mitochondria get healthier and stronger as you go through the protocol.  
Thyroid hormones improve mitochondrial functioning. Both of the active forms of B12 are critical for good mitochondrial health. Light and sleep are critical for healthy mitochondria.  
So that’s one part. Mitochondrial dysfunction is one underlying cause.  
And then there’s also HPA-axis dysregulation due to chronic stress and chronic biotoxins exposure. So chronic stress, trauma and biotoxins are other causes. So you need to address those as well. You need to follow the advice in the Step 4 and Step 5 modules to deal with the chronic stress and trauma and biotoxin parts of the equation. 
So no, I don’t recommend herbs or plants for adrenal fatigue. Because that’s just another band-aid approach. Adrenal supplements won’t get you anywhere in the long run. They don’t get to the root cause.