The episode begins with the last part of the last episode. The battle between the Daedalus and the two hive ships rages on. Sheppard is attacked by two Wraith Darts but another F-302 manages to destroy them. He doesn't have time to knock out the hyperdrive of the two ships so he orders the other F-302s back to the Daedalus just before the hive ships jump to hyperspace. Once they're gone it appears that Sheppard was killed as there is no sign of him but in truth he managed to latch on to one of the hive ships before they made the jump.
Meanwhile on Atlantis the Daedalus has returned and Dr. Weir is intent on dispatching it and the Orion to deal with the hive ships as soon as possible. Colonel Caldwell is reluctant because the Daedalus requires a lot of repairs and the Orion still doesn't have up its shields and weapons but Weir points out that they're the best chance Earth has of stopping these Wraith ships.
Rodney, trapped in a cocoon with Ronon, is bemoaning his fate while Ronon continues to struggle.
On board the hive Michael sees the hive queen and is infuriated that she didn't inform him of her plan to betray the team. She feels that his time as a human has made him weak and sympathetic towards them and says that she doubts that the stench of what he was turned into will ever truly go away. He finds out that he is restricted from different areas of the hive ship when he tries to visit one and returns to his quarters angry.
Weir communicates with Landry at SGC and he informs her she needs to come in person to brief the IOA. She comes through and tells them of her plan to use the Daedalus and the Orion to stop the Wraith ships and they don't agree, but she plans to stick the plan until they overturn her decision and they'll have to fire her to do that.
The hive ships drop out of hyperspace between the Pegasus Galaxy and the Milky Way Galaxy for 15 hours to let the ships rest. Sheppard attempts to contact McKay and Ronon over the radio but gets Michael instead. Michael offers his help because he knows that if he stays on the ship much longer that the Wraith will most likely kill him and he's willing to help Sheppard if it means staying alive. He directs Sheppard to where the best place to knock out the hyperdrive is so the ship can't leave or run if the Daedalus arrives. Sheppard complies but before he can knock out the hyperdrive of the second ship he is captured.
On the hive ship Ronon manages to cut himself and McKay free of their cocoons and they head to the nearest control station in order to cause the most amount of damage that they can to the hive ship. On Earth Weir gets a message from Atlantis saying that the Daedalus and the Orion are ready to go. Even thought the IOA still hasn't decided whether or not to go ahead with this plan Weir gives the go ahead and the Daedalus and the Orion jump into hyperspace.
Onboard the hive ship Michael takes Sheppard from his guards under the guise of interrogating him and then gives him back a gun before they go off to find McKay and Ronon. Meanwhile the Daedalus arrives and opens fire on the hive the team is on with every single nuclear missile that the Daedalus has. While the Darts stop most of them, one gets through and causes serious damage to the hive ship. Moments later the Orion jumps in, having managed to bring up its shields. They succeed in destroying the other hive ship with a salvo of drones, but sacrifice their shields to do so and eventually the crew is forced to abandon ship to the Daedalus before the Orion is destroyed by the first hive ship.
Soon after this Sheppard and Michael catch up with Ronon and McKay, returning their weapons to them and sabotaging the ship before heading in a Dart to the Daedalus which beams them aboard before the hive can destroy the Dart. Before they left Michael disabled the jamming codes for the ship but they have no more nukes to beam over. They manage to disable the hive ship by firing into the Dart bays, causing enough secondary explosions that the hive ship's weapons are disabled and it's severely damaged but their shields go down and one of the hive ship's shots hits the Daedalus causing serious damage to it as well. It knocks out life support and they have only 9-1/2 hours to fix it before they're out of air and that's not enough time. They decide to beam a canister of the retrovirus gas over to the hive and once the Wraith are humans capture them and beam the Daedalus' crew over until the ship's life support can be repaired. The plan works and the only Wraith they find is the Queen, who they quickly kill and take over the hive. The hive ship taken Sheppard tells Caldwell to start sending over the crew.
To Be Continued...