The episode opens inside a monastery, the sounds of Wraith Darts buzzing around outside, and several monks frantically hurrying around. They speak of the end if they are taken, just before they are taken.
The next scene we find Dr. McKay and Allina, an archaeologist, discussing the possible location of a ZPM on her planet Dagan. The other SGA team members seem bored with pouring through old ancient text, until McKay shows them an ancient charcoal rubbing that clearly shows an object that looks like a ZPM.
Back in Atlantis, McKay explains that according to legend an Ancient from Atlantis came through the Stargate and entrusted a sect of Suderian Priests with a rare treasure or Potentia. The Ancient said to keep it hidden from the Wraith at all costs. Because the Suderians worshiped the Ancients, the Potentia became their most sacred artifact. McKay believes the Potentia is a ZPM, and because the Suderians were just holding the ZPM, it most likely would still have a full charge. The bad news is that after 10,000 years of Wraith culling, the Suderian race is extinct. Dr. Weir agrees it is worth pursuing and sends them back to Dagan to continue their search.
The Genii however, have learned of the SGA search through an operative they have on the planet. Commander Kolya, believing it would be a mistake for Atlantis to get a new power source, plans a mission on his own to go to the planet and intercede.
On Dagan, Allina explains about the set up of the Brotherhood of the fifteen and the steps they put in place so the Potentia could be found should the Brotherhood be culled. The Priests created nine stone markers which would lead to the Potentia, of which three had been already found. From the markings on the three stones recovered, McKay is able to extrapolate where to dig to find the other six. After a lot of digging they find five more stones, but not the ninth and final stone. As they continue to dig for the ninth stone, they find a hidden underground chamber created by the Brotherhood. The team lowers themselves into the chamber and find a raised pedestal with markings corresponding to the stones they have recovered. The pedestal also has hand indentations on each side.
In Atlantis, while messing with control room equipment, Dr. Zelenka discovers that Atlantis' long range sensors have become active. Sensors they didn't know Atlantis had before. After working on this new sensor, Zelenka determines a Wraith Dart ship is approaching Atlantis. It will be there in 27 minutes.
On Dagan, Lt. Ford is standing guard over the chamber entrance when he is hit with a Genii tranquilizer dart. Kolya and his team take over the entrance, trapping Major Sheppard and his team in the chamber. After some verbal sparring, McKay offers to help the Genii find the ZPM, but only if the Genii promise not to hurt his people.
On Atlantis, things are getting tense as the Wraith Dart approaches. Dr. Beckett is called on to fly a third of three Puddle Jumpers, as he is the remaining person there with the Ancient gene. The Wraith Dart and the Puddle Jumpers fly at each other as the Dart approaches Atlantis. The Dart is able to destroy one Puddle Jumper immediately. The Dart then flies over Atlantis emitting a scanning beam. As the Dart leaves the city with the Puddle Jumpers in pursuit, it self destructs. Zelenka determines the Dart was relaying the scanning information, and says he will try to use the new long range sensors to see what is along the path the information was sent.
On Dagan, Allina realizes the symbols on the stones are not a gate address, but match the symbols on an ancient wall painting in the Monastery. After some work with the stones and the painting, McKay determines the ninth stone is not buried, but is actually contained behind the painting and pulls it out.
Back in the chamber, Sheppard and his group put together what they can from their equipment to use to fight with when Kolya's team returns. Kolya eventually returns with all nine stones, and orders his lieutenant to place the stones on the pedestal and retrieve the ZPM. His lieutenant does as ordered, but the pedestal captures his hands and marks are made on his palms. The lieutenant then falls over dead. Kolya, not to be discouraged, tells McKay to pick another stone combination and tells Sheppard he will be the next to try. It is Sheppard, not McKay though, that is able to determine the correct combination of the stones, and the ZPM pops out of the near by wall. It's at this point Sheppard's team, being held to the side, sets off a flash-bang grenade and takes control of the Genii team.
Sheppard and team strand the Genii in the chamber and leave with the ZPM. However, on the way to the gate to return to Atlantis, they are waylaid by a group of Daganians. Allina says she and the group are members of the new Brotherhood. She tells them the Potentia will be hidden again on another world, until the return of the Ancients, and tells the Atlantis team to leave.
Once back in Atlantis, Sheppard, McKay, and team learn that Zelenka, using the newly found long range scanners, has determined that three Wraith Hive ships are headed to Atlantis and will be there in two weeks.