John and Teyla are sharing a quiet evening together and as they have a drink, Teyla talks about how John rescued her from Michael and she always knew that he'd come for her. John smiles but then draws a blank, as he can't remember rescuing her. Lt. Aidan Ford appears, saying that John never rescued him either. John feels a sharp pain in his side and looks down to see blood leaking through his shirt… and wakes up to realize that he's buried in rubble with a piece of metal in his side. He and Ronon are buried under tons of rubble after Michael's compound self-destructed.
Elsewhere, McKay and Lorne are similarly trapped. McKay is uninjured but panicking, while Lorne is injured. They wonder if anyone else survived, and Lorne figures that the Daedalus should be there in three hours to rescue them. He figures that Lt. Edison, who was on outside patrol, is most likely to have survived and will take the gate back to Atlantis to bring help as well.
Michael's cruiser is often in space. He receives word that the compound self-destructed and orders his hybrid crew to set course back to the planet.
Lt. Edison returns by gate to Atlantis and briefs Sam on the situation. She orders Keller to prepare an away team to rescue their missing comrades.
McKay tries to keep his mind off of his claustrophobia by accessing Michael's database. They hear people moving above and yell for help, and Sam and her team start digging. McKay calls out that the database info indicates that Michael received a signal when the compound self-destructed. Sam has a Jumper go into orbit to keep watch and her team starts digging up Lorne and McKay.
Ronon pulls the piece of metal out of Sheppard's side, but John is still trapped beneath the rubble. Ronon refuses to abandon him and tries to free him.
Aboard his cruiser, Michael examines Teyla and notes that she should be giving birth any day. He says that he won't harm the child but doesn't say anything about harming her. He orders Kanaan to release her from her bonds and leaves, and Teyla tries to convince Kanaan to rebel against Michael's programming before he kills them all.
The rescue team frees McKay and Lorne and detects Ronon and Sheppard's life signs. However, Michael's cruiser enters orbit and once he senses their life signs, realizes they're looking for survivors. Sam gets her team into the cloaked Jumper just as a Wraith Dart launches an attack. They manage to bring it down but Michael dials the gate and establishes a wormhole to keep them from escaping back to Atlantis. Michael sends his hybrid soldiers down to find any survivors while McKay takes the Jumper into orbit. They figure Teyla is on-board but have no way to locate her on the ship.
Ronon and Sheppard are still trapped and hear digging above. They hear voices up above and call for help.
The Daedalus arrives and Caldwell's opens fire. Michael's ship returns fire but is unable to penetrate the Daedalus shields. Caldwell manages to disable is hyperdrive before it can abandon its Darts and escape into hyperspace.
Sheppard tests the new arrivals by asking them about their preference in beer. Realizing that Michael's hybrids are above, Ronon and Sheppard prepare to open fire when they arrive.
Caldwell's men detect Ronon and Sheppard beneath the rubble, but can't beam them up without dropping shields. At Sam's insistence, Caldwell reluctantly drops the shields and teleports them out in time, while McKay brings the Jumper into the bay. Michael's ship inflicts heavy damage and Sam and McKay are forced to start repairs. Sheppard is taken to the infirmary but despite his wound tells Keller to release him so that he can rescue Teyla. He and Ronon meet with Sam and McKay and they come up with a rescue plan. Sam orders Caldwell to launch a 302 attack. Michael responds by launching Darts, and Sheppard takes his team onboard Michael's ship in the cloaked Jumper when it drops its shields to launch.
The Daedalus manages to disable the opposing ship's weapons, giving them breathing space. Sheppard, Ronon, and McKay home in on Teyla's life signs and find her just as she goes into labor. Michael's crew completes repairs on the hyperdrive and prepares to leave. Sheppard and Ronon go to sabotage the drive with C4 while McKay tries to help Teyla as she starts delivering her son.
Sheppard and Ronon destroy the hyperdrive, alerting Michael that there are intruders on board. McKay successfully helps Teyla give birth, and Sheppard and Ronon arrive. They all go to the Jumper, only to discover that Michael's hybrids have discovered it. They try to find a data terminal, but stumble across Kanaan, the baby's father and Teyla's mate. She convinces him to help and he agrees to lead them out. Sheppard decides to trust him… once he gives them his weapon.
The Daedalus detects a Dart leaving Michael's cruiser. Sheppard, the pilot, hails them and informs them that he put the others into Wraith teleport storage and is holding onto the baby rather than risk its health. Now that he knows they're safe, Caldwell orders the destruction of Michael's ship while Sheppard takes the Jumper down to the planet to take the gate back to Atlantis.
Later, McKay is going to visit Teyla when he runs into Sam. She tells him that the IOA has recalled her to Earth for an evaluation. He congratulates her on her performance as base commander. In the infirmary, Keller prepares to take Sheppard into surgery, while Teyla informs him that she'll be naming her son Torren John Emmagan, in honor of her father and John.
Sam arrives back at SGC and meets Woolsey, who informs her that she is being removed from command, and he'll be taking command of Atlantis.