Sheppard's team goes to the planet where the people of Taranis have been relocated. They find no one there, and an underground facility under the village. They find an empty cocoon and figure something is roaming the tunnels. They make contact with Weir and let her know what's going on, and she sends in a team to provide backup for them.
The team finds the corpses of the missing Taranians, all killed with neck wounds that are strangely familiar. Ronon finds an Iratus bug and they figure a Wraith was doing experiments. The lifesign approaches them while the marine squad led by Lt. Negley contacts them. They are attacked by a large bug like creature and barely escape Meanwhile Negley and his team is captured by a Wraith fighter.
The bug creatures start to emerge from the cocoons, and Sheppard is forced to sue explosives to destroy them. When Sheppard and his team go back to the gate, they discover that a control crystal has been removed from the gate control panel. They are stranded. Without the crystal, they cannot dial Atlantis. They are unaware that a Wraith is in the tunnels: their old "friend" Michael.
Sheppard's team returns to the settlement tunnels and they pick up a second previously undetected lifesign. Teyla is cut off from the others and a gas pipe bursts, spewing out thick clouds of gas which the creature uses as cover. They manage to kill it while Teyla is confronted by Michael. Sheppard, McKay, and Ronon get the door open only to find Teyla gone.
Michael straps down Teyla and reveals that he is responsible for the breeding project. Hunted by both humans and Wraith, Michael plans to create a race of insect soldiers to defend him. He explains how he used the Iratus bugs to absorb huge amount of human DNA, then accelerated the development and augmenting its physiology. While the team tries to get to Teyla, Michael leaves her to the creature. Sheppard uses C-4 to blast through the doors and Michael sends his creature to kill them. He then explains that he captured the marines and forced Negley to tell Weir that the Taranians relocated and everything is fine. Michael then unleashes an Iratus bug to feed on Teyla.
Sheppard's team finds the dead marines, then the creature attacks McKay and they manage to kill it. They find Teyla just in time to kill the Iratus bug, and Ronon and Sheppard go to hunt down Michael while Rodney tries to access the computer systems. He shuts down the EM shielding and reestablishes contact with Sheppard. He is also able to fully scan the base and picks up dozens of lifesigns near Sheppard. Michael releases them and they head for Sheppard.
Sheppard confronts Michael in a Mexican standoff and the major demands the control crystals. Michael drops his gun then runs as a creature attacks Sheppard. Ronon kills it and the two go after Michael. McKay and Teyla climb for the surface while Sheppard and Ronon fight a rearguard action. They get to the surface and Sheppard takes Michael's ship then beams out Ronon. Michael stuns Teyla and McKay but Sheppard beams them out and flies to another planet to ditch the Dart and return to Atlantis. They brief Weir on what happened and ask for the Daedalus to make another stop along the way.
Later McKay analyzes Michael's data and determines that Michael has created hundred of the creatures. The Daedalus scans the planet but finds nothing, and they realize that Michael will be coming for them.