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An unknown armored man appears on the command deck of the Andromeda and engages Dylan in combat. When defeated, the man shatters into dark matter particles that infect the Andromeda's guidance system.
A stowaway creature is discovered devouring the Maru's electronics. Unable to stop the creature from moving to the Andromeda and reproducing, the crew must find the creatures before they permanently cripple the ship.
In an alternate timeline, Gaheris Rhade takes command of the Andromeda and attempts, with the aid of the crew of the Maru and a hologram of Dylan, to reestablish the Commonwealth and drive back the Magog threat.