Sheppard, McKay, Teyla and Ronon visit an oppressed, poverty-stricken village that sacrifices half of every harvest to a mysterious Lord Protector in a great tower - a tower that looks exactly like the central spire of Atlantis.
In exchange for the farmers' tribute, the Lord Protector defends them from the Wraith with amazing weaponry. Intrigued, Sheppard's team guesses that the tower, an Ancient relic, must be well-stocked with valuable drone weapons. As McKay sneaks closer to investigate, Otho, the Chamberlain to the Lord Protector, arrives in the village. He scans Sheppard, Teyla, and Ronon with an Ancient device, then forces Sheppard to surrender his gun and pay a visit to the tower.
Inside this unsettling copy of Atlantis, Sheppard meets the elderly Lord Protector; his surly son, Tavius; and his attractive daughter, Mara. The Lord Protector quickly grows so weak that he must retire to his chambers to rest. Obviously, one of his children will soon inherit his throne.
That evening, Mara aggressively tries to seduce Sheppard. Unnerved, Sheppard seeks answers from Otho, who explains that the royal family carries the Ancient gene that allows them to operate the tower's technology. Despite generations of selective breeding, however, the family's abilities have deteriorated. Recently, when Otho scanned the team, he discovered that Sheppard also possesses the gene. Thus, the Lord Protector promised to designate Mara his successor ... if she can revitalize her family's genetic future by marrying Sheppard.
Rather than consent to a lifetime of wedded bliss and feudal lordship, Sheppard summons Dr. Beckett. Beckett investigates the Lord Protector's mysterious weakness and offers to treat Otho with his gene-therapy regimen, which allows recipients to operate Ancient technology. Otho is deeply unsettled by the implications of the drug, which could revolutionize the planet's rigid class structure by making "royal" power available to countless peasants.
Meanwhile, McKay discovers an entire city - just like Atlantis - buried beneath the tower. He sneaks into its earthquake-prone corridors, hoping to shut down the ZPM that's powering the royal family's advanced technology. At the same time, in the village, Ronon kills a royal constable for abusing a woman; his action inspires the downtrodden peasants to rebel and demand their rights.
Back at the tower, the Lord Protector dies just as Beckett concludes that the man was poisoned. The royal court, with an unknown murderer in its midst, plunges into a succession struggle. Worse, the surprise winner then decides to consolidate royal power by making a deadly example of Sheppard, his team, and the entire nearby village.