"Infestation"

The Phoenix’s science labs were working on the use of nanites for repairs when the microscopic creatures evolved and gained sentience. The nanites utilised the Chief Operations Officer and the Captain to communicate, refusing to parley with the organic officers aboard the ship and fearing for their survival. They took over the computer and began to shut down the systems, but eventually were convinced to co-operate so that the crew could safely rehome them and ensure that they were acknowledged as sentient beings with free will.