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The synaptic pathways were an area of the brain.
In January of 2154, Jonathan Archer's synaptic pathways were infiltrated by a unique neurochemical, causing him to become protective of an Xindi-Insectoid hatchery at the expense of NX class starship Enterprise NX-01 and its mission into the Delphic Expanse. (ENT: "Hatchery")
Later, in February of 2154, Starfleet officer Hoshi Sato was kidnapped from her post on Enterprise by Dolim's order. Sato's synaptic pathways were altered through a series of parasitic injections into her neocortex. This was to force Sato to break the Xindi-Aquatic encryption protocols, giving Dolim the launch codes to the Xindi weapon. However, Sato initially proved to be resilient to the treatments, and attempted suicide rather than break the encryption protocols. After being recaptured, Sato was given further injections to make her more compliant. (ENT: "The Council", "Countdown")
After her assimilation in 2356, Annika Hansen was placed in a Borg maturation chamber where the hive mind began to restructure her synaptic pathways, leading to her eventual emergence as a Borg drone. (VOY: "Collective")