With Atlantis' rations dwindling and the crops on the mainland months away from being established, Dr. Elizabeth Weir concentrates her efforts on trading with other worlds for food. Maj. John Sheppard feels they should be looking for allies against the Wraith, but he goes on a trading mission with Dr. Rodney McKay, Lt. Aiden Ford and Teyla - who introduces them to the Genii, a simple farming people. Though the Genii have traded for years with Teyla's people, the Athosians, they are wary of Sheppard and the others.
Cowen, their leader, is tempted by the medicine the Atlantis team offers, but he wants more, claiming that more land will have to be cleared of tree stumps before the Genii can replant enough crops to replace their stores - a task that will take an enormous amount of time. Sheppard blows up a tree stump with a small C-4 plastic-explosive charge: Problem solved. But now Cowen wants the C-4 and the medicine.
Teyla and Ford remain behind for the Genii's "harvest ceremony" while Sheppard and McKay fly their puddle jumper through the stargate back to Atlantis, where Weir reluctantly approves Sheppard's request to form a pact with the Genii.
Upon returning to the Genii planet, McKay picks up radioactive readings - quite unusual for an agrarian world. He and Sheppard follow the readings to a metal hatchway that leads to an underground bunker - and to an amazing underground city, where they are intercepted by Cowen (who now wears a uniform instead of farming clothes) and heavily armed Genii soldiers.
Normally, Sheppard and McKay would have been killed for discovering the Genii's secret - that they pretend to be primitive farmers to avert suspicion while they prepare to resist the next Wraith culling. But Cowen is curious about just how much more helpful information he can extract from the Atlantis personnel.
Sheppard goes out on a limb and asks if the Genii would like to have allies against the Wraith. Cowen is intrigued. McKay has, by now, figured out that the Genii are working on a nuclear bomb with which to counterattack the Wraith, and that they need the Atlantis team's C-4 to complete their atomic trigger. McKay says he can help them.
Suddenly, Sheppard and his team are no longer prisoners; they are ushered into the Genii's great meeting room, where Teyla and Ford have also been brought. Cowen explains how, before the next culling - which the Genii think won't happen for a few more decades - the Genii will locate the Wraith's hive ships and destroy them with nukes while they hibernate. Before he can go on, Teyla and Sheppard drop their own "bomb" - the Wraith are already awake, and Atlantis is to blame. Cowen's mood turns sour again, but Sheppard tells him they have weapons beyond the Genii's imagination, as well as a space ship. If they work together, they can beat the Wraith.
Cowen is convinced and lets the Atlanteans in on the Genii's master plan: They have salvaged, from a downed Wraith Dart during the last culling, a Wraith data-storage device that contains information about the hive ship from which it was deployed. One of their scientists, Tyrus, has used it to find the 'gate address where a hive ship still sleeps. The plan is to sneak aboard the ship and download data containing the whereabouts of the other Wraith ships, which the Genii will later destroy with their nuclear arsenal.
Back at Atlantis, Weir responds to the plan with a resounding "No!" Sheppard and Ford calmly lay out the reasoning behind it, and she eventually agrees to an intelligence-gathering mission only.
Sheppard and team take Cowen and Tyrus to the Wraith target. Deep inside the Wraith hive ship, they find humans cocooned for future Wraith feedings. Teyla wants to save them. Tyrus refuses on the grounds they can't risk awakening this ship's Wraith. When she tries anyway, Tyrus shoots one of the cocooned humans. Wraith guards come and shoot Tyrus in return. Cowen, Sheppard and McKay successfully download the data they need, then rendezvous with Teyla - who gives them the news about Tyrus as they head back to the Genii planet.
There, Cowen and his men converge on Sheppard's team. Cowen wants the intel and the jumper - or else. Sheppard, who suspected Cowen would pull something like this, orders two cloaked jumpers that have been hiding overhead to decloak and fire on his command. He takes back the download device from Cowen and returns to Atlantis.
Though Sheppard has failed to make an ally of the Genii, the data they obtained reveals valuable information: There are more than 60 Wraith hive ships, and possibly many others. Sheppard and Weir can only hope they don't all attack Atlantis at once....