The Siege, Part 2

"The Siege, Part 2" is the twentieth episode of the first season of Stargate Atlantis.

Plot
Dr. Rodney McKay has returned to Atlantis and Dr. Elizabeth Weir orders the self-destruct activation. As they attempt to dial the Alpha site, the Stargate is suddenly activated; the 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 Dillon Everett who instantly takes over command. He informs them that they are here to defend Atlantis at all cost, and that they have brought weapons and equipment with which to do so. McKay concludes that Stargate Command found a Zero Point Module and Everett informs him that the Daedalus will arrive in four days with it.

In the conference room, Everett informs the others about their plan, but Weir is only allowed to join after Major John Sheppard insists. They are informed that they will use advanced Railgun weapons originally intended for use on Prometheus, and eight Naquadah-enhanced 1200-megatonne Nuclear warhead as stealth space mines. Along with these, they have brought a Mark II Naquadah generator, which is capable of a 600% power increase over Atlantis' Mark I reactors, and was designed to power the Control chair. After the meeting, the railguns are deployed and the mines are laid in space by cloaked Puddle Jumpers. Meanwhile, Everett visits Teyla Emmagan in the training room and orders her to stay out of the way, cementing the distrust surrounding her.

After considerable tinkering, McKay is able to link the new reactor to the weapons chair, and the platform is activated by Dr. Carson Beckett. McKay subsequently discovers that there are only a few dozen Drone weapons left. The remaining multi-thousand were used during the original siege 10,000 years previously. Without warning, there is an alarm; the Long range sensorss have detected hundreds of asteroids heading straight towards the proximity-activated nuclear bombs. McKay assesses that the rocks were launched by the Wraith, who have somehow discovered the mines. With no way to deactivate the warheads, the locater signals of all eight warheads vanish on the display as the mines detonate, with the Wraith at a safe distance. The radiation causes interference that disables the sensors.

Later, Everett meets with Sheppard in the Holo room and Sheppard grimly plays the history of the galaxy. Everett then informs him that he read the report Sheppard submitted surrounding the events in Rising. He explains that Colonel Marshall Sumner was a personal friend of his and that he is outraged with Sheppard for killing Sumner. Suddenly they are informed that there are approaching Wraith Darts and the battle for the city starts. Marines man the railguns and Sheppard takes the Chair; thanks to the Drone weapons and the railguns the first wave of Darts are destroyed but some parts of the city are hit.

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. Suddenly Teyla enters and informs them that there are Wraith in the city, who had invaded during the first wave. Together with a group of Athosians, the military starts to search for them. Meanwhile Weir gates to the Genii world, but is captured by them and held hostage. They want to exchange her for the C-4 they have been cheated out of, however Weir is able to convince them that they will use the C-4 only to test the devices, while they could be used for their true purpose of destroying the Wraith. The Genii finally agree and supply the Atlantis team with two nuclear devices. The hunt for the Wraith is going badly, as the Wraith have begun damaging and destroying the Naqahdah generators powering the City. To make matters worse, McKay soon discovers that the Genii nukes are incomplete; he and Zelenka are soon in a lab completing the weapons against their fatigue, much to Beckett's disagreement.

At Atlantis the test-run of Sheppard's plan is a success, so McKay and Zelenka start to install the completed weapons into the Jumpers. Meanwhile, several men are taken out by the Wraith and the wounded are taken to the Alpha site. A second wave of Darts appears without warning; Sheppard mans the control chair to take control of the Jumpers. After several attempts at initializing the Chair, McKay realizes the reactor has depleted its supply of Naqahdah. Desperate, Sheppard decides to fly the Jumper himself in a hive ship, much to the shock of Weir.

As Weir cannot stop him, Sheppard rushes to the Jumper bay and takes it up. Outside, as Lt. Aiden Ford's team attempt to repel the Darts, a group of Wraith materializes in front of them. Inside, Everett's team is overrun and he is cornered by a Wraith. Out of ammo, the alien begins to feed off him. The final scene of season one sees Sheppard heading undetected into the Hive's Dart Bay, the nuke armed, while back in the control room, McKay counts down until detonation.

Notable Quotes
(The Atlantis base has just activated a self-destruct, only to have several personnel from Stargate Command arrive to help them)

Everett: Good! Now does somebody want to please turn off that self-destruct?

(The Wraith have used asteroids to detonate several mines prematurely.)

McKay: Your mines make one hell of a bang, Colonel, I'm sure the Wraith's ears are ringing.

McKay: Look, you show up here with your guns and your brush cuts, but when it comes to actually saving the city, you turn to the scientists. And every time, what you ask is impossible.

Everett: When was the last time you slept, Doctor?

McKay: D-d-d-d…shut up, I have an idea

Ford: How about next time you can be the bait?

Sheppard: Yeah, next time. Maybe...

(McKay is trying to get a reluctant Beckett to sit in the Ancient chair)

McKay: It's out of drones; you couldn't do any damage if you wanted to, now SIT DOWN.

Beckett: You wanted to see me Rodney?

McKay: Yes yes. I need something to keep me awake.

Zelenka: Yeah, me too.

Beckett: I've already given you something.

McKay: (irritated) Yeah? Well we're building nuclear bombs here. Staying awake is sort of a prerequisite.