Botox blocks the release of neuropeptides/neurotransmitters from the sensory free nerve endings in exactly the same way as it blocks the release of Acetylcholine at the neuro-muscular junction. Ths reduces the sensory tone going to the brain. In migraines you are primarily blocking the fibres from V1 trunk of the trigeminal nerve, but also the cervical nerves.
These project to the same place in the trigemino-cervical tract and reduce the excitability state of the neurones, which in turn reduces the follow-on stimulation of higher centres
Interestingly, botox does not pass from neurone to neurone (unlike tetanus toxin) and stays only in the neurones that it enters at the site of injection. Using immunofluorescence techniques to show traces of botox in both the brain stem and the areas of meninges where V1 innervates because the individual fibres each have 3 branches from the nucleus in the trigeminal ganglion. skin, brain stem and meninges
Essentially, migraines are a generalised neuronal hyperexcitability disorder, and Botox reduces the level of hyperexcitability
You can read more on improving the botox treatment protocols in my paper included in my profile here. Honestly the PREEMPT Protocol is rather old hat since Allergan patented all that it could, and this blocked further commercial research into better botox protocols. In my experience, targeted higher doses of Botox into the glabella is equally as effective as the PREEMPT Protocol. PREEMPT thus doesn't reach the highest number of free nerve endings in the enthesis (attachment of the corrugators to its glabellar fascial compartment) of the glabella.
I hope this is useful
Go to: https://www.researchgate.net/profile/Chris-Blatchley