Sheppard and his team, accompanied by Dr. Keller, take a Puddle Jumper on a diplomatic mission and rendezvous with a Hive ship. They receive docking instructions and enter the ship's landing bay, where they are greeted by armed Wraith soldiers. Their Wraith ally, Todd, arrives and offers his apologies. He takes them to a meeting chamber and introduces them to his second-in-command. Keller explains that they have accessed some of Michael's reach and have developed a therapy that will remove the Wraith's need to feed on humans. Todd is skeptical and Keller notes that they aren't sure if the alteration would strip the Wraith of their other abilities. Keller needs test subjects and Todd considers their offer. He informs them that he'll agree to the treatment if it proves successful, but he doesn't have enough influence within the Alliance to convince the others. There is one they need to convince, the uber Wraith Queen, the Primary. However, she'll only speak with another Queen and Todd's died above Atlantis. He fooled the other Wraith into believing she was still alive. However, he has a plan… involving Teyla.
Back on Atlantis, Sheppard is skeptical of Teyla's involvement but she insists on going ahead. Todd arrives via the Stargate to act as technical advisor and Ronon warns him that he'll pay if anything happens to Teyla. Keller administers the treatment and after a few hours, she is transformed into a Wraith Queen in appearance.
Teyla takes the throne on Todd's ship and he coaches her on how to adopt the proper mannerisms and bearing. He lets Sheppard and the others know they've made contact with the Primary and that she's taken recent losses which will force her to consider survival as necessary. They rendezvous with the Primary and Teyla bluffs through the initial contact. She and Todd go to the Primary's ship where they meet with its Commander. The Commander takes his ship into hyperspace for security reasons and Teyla has no choice but to go along with the change in plans. Sheppard and the others get word of the change and confront Todd's second-in-command, who assures them he knows nothing of any betrayal.
Teyla and Todd are left alone and Todd assures her they're in no danger… for now. The Primary arrives and questions Todd's involvement, but Teyla refuses to back down. The Primary relents… and Todd cuts her throat. He puts the knife in Teyla's hand and asks for her forgiveness and tells her she needs to take claim for the kill and convince the crew she's suitable to replace their dead leader. The Commander arrives with his men and challenges Teyla, and then puts a knife to Todd's throat when he tries to speak for her. The Commander accepts her authority… for now, and they drop out of hyperspace on Teyla's orders to run a diagnosis.
In private, Todd explains that the Primary would never have accepted their proposal and that their culture is different: Teyla needed to claim ownership of the murder. He didn't inform her because he figured (correctly) she wouldn't go through with it. Todd tells Teyla she's now in control of the alliance and she'll have to stay in command until things are closer to normal.
Sheppard, Ronon, and McKay are still waiting and Sheppard believes that things are as they seem and the second-in-commander, which they've nicknamed "Kenny," is being honest with them. Kenny informs them they've picked up a signal from Teyla and they head for the indicated coordinates.
The Commander reports to Teyla that they've detected another Alliance's ship culling one of their feeding grounds. Todd calls for a private meeting with her, causing the Commander to wonder what's going on. Todd advises Teyla to respond to the raid or arouse suspicion, and assures her his ship will track them when it arrives. Teyla has no choice but to order them to respond to the raid.
Sheppard and Ronon come up with a plan to rescue Teyla by launching a diversionary attack on the other ship when they arrive.
Teyla's ship reaches the feeding ground and Todd advises her that the opposing ship will try to negotiate. Ignoring him, Teyla orders the Commander to disregard the other ship's hails and charge up the weapons. They open fire while Todd secretly questions Teyla, who insists she's keeping up the charade. The other ship returns fire and Teyla orders the Darts released, and Todd realizes she's trying to kill as many Wraith as possible. Heavy losses are incurred on both sides.
Todd's ship arrives and discovers that Teyla's ship has moved to the feeding grounds. Sheppard decides to have Kenny drop them off and they'll take the Jumper through a Stargate to the planet.
Teyla's ship loses weapons and its Darts are quickly overwhelmed. She continues the attack while Sheppard and the others arrive via Stargate and realize what's going on. Sheppard attacks the opposing Alliance ship from cloak and it blows up. Teyla takes credit for the victory but the Commander is astonished at the unpredicted victory. Meanwhile, Sheppard lands the cloaked Jumper in the landing bay along with the returning Darts. They move through the ship but are forced to open fire on soldiers moving past their position. They take out the first squad of soldiers but are quickly captured and the Commander arrives to imprison them.
The guys wake up in a cell and Teyla comes to visit them. She sends the guards away and tells Sheppard and the others that she's Queen of the Hive, and they shouldn't try to attempt. She refuses to leave with them until she's solidified her position. Sheppard agrees… but they're unaware the Commander is listening in. He goes to see Teyla in her quarters and ignores her orders to leave. The Commander attacks her and prepares to cut her throat, but Todd arrives and kills him.
Todd's ship arrives and he transfers Sheppard and the others. Teyla departs after leaving Todd in command in her absence. As she goes, Todd assures her that she's allayed all suspicion but they should let matters settle for a while. Teyla wonders if he plans to break their agreement and warns him that she'll be watching him. If he steps out of line, she'll have him removed… permanently.
Later on Atlantis, Teyla is restored to normal. Sheppard informs her that Todd has solidified his position with the Alliance and is due to meet with them in a few weeks. Teyla wonders if they're playing into Todd's scheme but Sheppard believes they're still better off.