4 ideas
The mitochondria in Kiyomi's cells turn out to have gained awareness, to have engineered her death, and to be spreading through the lab culture and the transplant recipient. Their goal is to produce a new being whose body the mitochondrial genome controls instead of the nucleus.
They still carry their own small circular DNA, divide on their own schedule, and pass down only through the mother's egg. Because of this separate genome and separate line of inheritance, they have a biological interest distinct from their host's, so a mitochondrial 'revolt' is a real symbiosis breaking down.
Reverse the usual question of what the cell uses mitochondria for, and ask what mitochondria use the cell for. Seen this way, the human body looks like a habitat and transport system built to carry and multiply mitochondrial DNA. Human agency becomes a side effect of a molecular tenant's interests, and it is no longer clear which partner is the parasite.
Mitochondria make ATP by pumping protons across a membrane and then letting them flow back through ATP synthase. If they let protons leak back without making ATP, the energy is released as heat, which is how brown fat keeps the body warm. The novel pushes this uncoupling mechanism to an extreme, so that mitochondria in control of a body's energy supply can make it burst into flame from within.