The Siege (Stargate Atlantis)

While the Wraith come closer to Atlantis, the leading group of the expedition is informed by Rodney McKay and Radek Zelenka that the Wraith will pass the last Lantean defence satellite; they are very confident they can bring it back online and obliterate all three Hive Ships before they even reach Atlantis. McKay volunteers for the mission to power it up, entering the airless, weightless environment with a Naqahdah generator tethered to him, with it bobbing about like a helium balloon on the end of a string in an atmosphere within a gravity well. Meanwhile, Elizabeth Weir, John Sheppard, his team, and Bates search for a new Alpha site. Weir is informed by Zelenka that the self-destruct of the city wouldn't destroy enough of the city to prevent the Wraith from tracing them back to Earth. He shows Weir a simulation which predicts that the Wraith will be able to recover some of the City's technology, and some of the database. After an attack by darts on Atlantis and subsequent unexplained faults, it is suspected that one Wraith has infiltrated outlying parts. With a biometric sensor they are able to locate the Wraith and they try to capture him. However, the Wraith is able to fend off Sheppard's team until he is stunned by Aiden Ford. The Wraith is imprisoned and Sheppard starts to interrogate him after he named him Bob, but he keeps silent.

Meanwhile, the Wraith Hive-Ships drop out of hyperspace as predicted, and Grodin powers up the satellite. McKay watches from the cloaked Puddle Jumper as the energy beam from the weapon successfully slices through and destroys one Hive-ship. Amid the celebration, Grodin radios that he is having trouble - McKay's rerouting has overloaded and the weapon can't be fired again. Grodin cannot bring it back online, and as McKay orders the pilot to rescue him, the remaining Hive Ships destroy the satellite, killing Grodin. McKay can't do anything, thus he informs Weir and is ordered to return to Atlantis. Weir informs the base about what has happened and afterwards starts the self-destruct countdown. Having heard the evacuation order, Bob tells them no matter where they go, no matter where they hide, the Wraith will find them, as well as Earth.

Rodney McKay returns to Atlantis, where Elizabeth Weir orders the self-destruct activation. As they attempt to dial the Alpha site, the gate is suddenly activated; a wormhole was established from Earth. Much to everyone's amazement, a company of marines come through and Weir and the others are greeted by Colonel Dillion Everett who instantly takes over command. Everett informs him that the Daedalus will arrive in four days with a Zero Point Module (ZPM).

In the conference room Everett informs the others about their plan, but Weir is only allowed to join after Sheppard insists. Later Everett meets Sheppard in the holographic archive and Sheppard grimly plays the history of the Pegasus Galaxy. Contemplating strategies, Sheppard suggests that they remotely control the Puddle Jumpers using the Chair and fly them, cloaked, into the hive ships armed with an explosive; he believes they should ask the Genii to use their nuclear weapons. At Atlantis the test-run of Sheppard's plan is a success, McKay and Zelenka start to install the completed weapons into the Puddle Jumpers. Meanwhile, several men are taken out by the Wraith and the wounded are taken to the Alpha site.

As Weir cannot stop him, Sheppard rushes to the Puddle Jumper bay and takes it up. Outside, as Aiden Ford's team attempt to repel the Darts, a group of Wraith materialises in front of them. Someone lets off a grenade, and Ford and a Wraith are catapulted into the ocean. Inside, Everett's team is overrun and he is cornered by a Wraith. Out of ammo, the alien begins to feed off him.

John Sheppard’s efforts to pilot a Puddle Jumper with a nuke on board to destroy a Wraith hive ship result in success, but he does not die. The Daedalus arrives and rescues Sheppard by the means of Asgard teleportation, and later uses the same technology both to deliver the Zero Point Module to Atlantis and to deploy another nuclear bomb onto the third and final hive ship, destroying it. First Lieutenant Aiden Ford becomes paranoid after realizing the Atlantis team is afraid of him because he has been injected with the Wraith enzyme and escapes through the Stargate in one of the Puddle Jumpers. It is discovered that twelve more hive ships are on their way to Atlantis. Daedalus attempts to intercept them, destroying two ships in the process, but is forced to retreat after the Wraith activate countermeasures which make it impossible to teleport nukes onto them. The Wraith then begin bombarding Atlantis again. A plan is made to beam a nuke directly above the city and then cloak the city, to make the Wraith think that Atlantis self-destructed. This plan works, and the Wraith fleet leaves.