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.

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.

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.

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.

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.

In the original script, Colonel Dillion Everett was supposed to be a recurring character in the series future along with his two United States Marine Corps officers Major Ferrell and Captain Radner, the announcement also suggested the involvement of Dr. Radek Zelenka.

The producers chose "Radek", a fairly common Czech given name, without input from portraying actor David Nykl.

[3] At the end of season 1, Rainbow Sun Francks (portrayed Aiden Ford) was disappointed about the evolution of his character, he then asked the producer if they could expand him somehow.

When developing part three of "The Siege", Brad Wright and Gero handed over a copy of the script to director Martin Wood.

In the last scene, where John Sheppard is stalking Aiden Ford, the portraying actors Joe Flanigan and Francks complained about their characters getting "Off a little easy."

While the show was not a success, together with Battlestar Galactica and Stargate SG-1, it made the Sci Fi Channel the top rated cable network in the United States for the 18–49 and 25–54 demographics.