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In Galaxy-class starships the main computer was based in three computer cores; each of the cores could run the ship alone. The triplicate system allowed the ship a full backup should anyone core be damaged, and allowed the two parts of the ship to fully function when using the class' saucer separation feature. When not separated the two cores located in the class' saucer section ran at 100% redundancy, allowing the ship to continue normal operations instantly should one core go offline. The engineering section core served as backup when the ships of the class were not separated. (TNG reference: Star Trek: The Next Generation Technical Manual)
On stardate 24.09.45, the USS Enterprise's main computer was remotely hijacked by a race of robots, who remote controlled the ship and then forced it to land on their planet where they hoped to take the Enterprise's power rods to refuel their own power units. Until a member of crew spotted the planet as the ship got close, the crew were unaware they were even being remotely controlled. (TOS comic: "UK comic strips, first story arc")
In 2381 the Sentry SecondGen White-Blue entered the computer of the USS Titan, and sensing an potential for intelligence in the ship's main computer encouraged it to develop. As a result Titan's main computer began to reprogram itself, and eventually developed a persona, the Titan Avatar, which could holographically manifest itself throughout the ship. (TTN novel: Synthesis)