Guardians are autonomous Elder spacecraft, tasked with protecting sensitive Elder systems such as those powering the Galactic Shield like the Roach Motel. The Guardians will attack any spaceship that attempts to pass through the shearing field at the edge of the protected system, unless a valid Elder authentication code is broadcast.
While the Guardians do not possess an AI with the intelligence to rival a Master Control AI like Skippy, their Elder programming does mean they are clever, and they can adapt quickly to attempts to circumvent them. Guardians are small, and not overwhelmingly powerful craft when dealt with individually, but when combined into a swarm, they are formidable.
The Merry Band of Pirates encounter the Guardians when they enter the Roach Motel. They initially accept the authority of Skippy as an Elder AI and do not attack the Flying Dutchman (which is heavily damaged by the shearing field), but become increasingly frustrated with his inability to explain his purpose in the system. They eventually chase the Pirates out of the system, and immediately attack the next time they attempt to return.
SPOILER ALERT!
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The Pirates encounter a dead Sentinel in the Roach Motel. When investigating the wreckage, The Flying Dutchman is infected with an energy virus. Skippy later speculates that the energy virus is a weapon wielded by the Guardians, specifically for the purpose of destroying rogue Sentinels which enter protected systems.