I'm not the most fluent person here, but can try to summarize just a portion.
Naviaux is looking at the cell danger response system. Any sort of stress can trigger a CDR, which involves ~30 different metabolic processes. Different diseases have signature metabolic profiles during CDR. His tests could accurately determine ME/CFS vs. control at ~95% (differed based on sex a smidge).
During CDR, the cell's channel receptors react by discharging ATP. This causes the mitochondria to produce more ATP, which can exhaust resources within the cell. Also, oxygen begins to build-up with in the cell leading to oxidative stress. He says that mitochondria are not defective in ME/CFS, but rather just responding to the CDR system to protect the cell.
Naviaux is looking at chronic illness as a lack of completion in the healing process. One idea is to try to use an antagonist to block the channels that are ejecting the ATP. He is going to trial the drug suramin, to interrupt the CDR process.
After blocking the ATP outflow, nutrients need to be reintroduced into the metabolic process in a timed and individual way that caters to one's unique metabolic needs. He has no general advice to PWME about how this can be accomplished as we are all highly individual.
The idea is to sort of wake-up the cells from a hypo-metabolic state.
There is a lot more, but you can compare a bit of what I said with his powerpoint attached in an above post.