On a relatively primitive planet, Sheppards team find the planet is protected by a tower, controlled by the Lord Protectorate and his family. They soon realise that the tower, is exactly like the central spire of Atlantis. From the villagers they realise that the tower has been used to defend the planet and the people from the Wraith, however they also use it to instill fear among the population.

The soon meet Otho, the chamberlin to the Lord Protector, who scans the team and discovers that Sheppard has the Ancient Gene which is needed to use the powers of the tower. He takes Sheppard to the tower, whilst leaving the others in the village. In the mean time, McKay discovers that the tower is only part of the structure, and the structure is infact as big as Atlantis itself.

John meets with the protectorate to find that he controls the tower and instills fear using the Ancient chair, which requires the Ancient Gene to be activated. However, the Protectorates son, and next in line to the throne, isn't happy about Sheppards presense on the planet. Sheppard soon discovers that Mara, the daughter of the Lord Protectorate, wants to wed him, and hence become the next Lord Protectorate as he has the Ancient gene, which is stronger in him, than any others that have lived on the planet, in the past 300 years.

With the Lord Protectorates' health deteriating, Sheppard hopes to buy him time by asking that Beckett be allowed to have a look at him, which the chamberlin agrees to. Beckett soon concludes that the Lord Protectorate has little time to live. In the meantime, the Chamberlin takes Sheppard to see the Puddlejumpers, and realises that Sheppard knows alot more than he's letting on. Sheppard offers Sheppard offers the chamberlin another option, he offers them a chance to have the Gene Therapy, which would allow half the villages to use the chair, in exchange for the drones.

In hopes of getting a few Drones to power the chair in Atlantis, McKay and his guide, venture into the catacombs of the tower to see how many drones are remaining. He soon discovers that theres plenty of drones remaning in the tower, enough to help save Atlantis if the Wraith come back. However, before he can leave the catacombs, cave in, causing them to be stuck with no way to contact the others.

Back in the village, a duel between Ronan and the Protectorates soldiers leaves the soldiers injured, and the Constable killed, causing the villagers to start an uprising. In the meantime, Sheppard is told that the Lord Protectorate has been killed, and that his son, will become the next protectorate anytime now. He tells Sheppard to leave, and save himself, and Sheppard agrees, and gives Othos the Gene Therapy potion in hopes that he can bring inequality amonst the people. In a last effort to save Mara before her brother has her killed, Sheppard goes to her, to ask her to come with her, however, he soon realises that Othos has other plans.

Othos imprisons Sheppard and Beckett, along with Tavious. They soon learn that, the Lord Protectorate was actually killed by the Chamberlin, Othos, and with the Gene Therapy, he will become the next Lord Protectorate. Stuck underground, McKay learns that the ZPM is near enough depleted. He uses the drone to blast a whole through the roof, allowing him to contact Teyla and Ronan. Back in the tower, Mara brings Sheppard his radio, allowing him to contact McKay.

With Othos in power, he activates the chair and sends the dones to the city, however to save the villagers as well as Teyla and Ronan, McKay uses the Star Drive of the tower to completely deplete the ZPM rendering the drones harmless, and the chair powerless. Sheppard and Beckett manage to escape, and face Othos, who tries to kill Shepard, however, he is stabbed by his own poison tipped blade and dies.

Sheppards team manage to get drones to protect the city, as well as a few puddle jumpers, and in exchange they offer the people of the village, medicine, food and help in creating a new order, one with equality.