The Siege, Part 3

"The Siege, Part 3" is the first episode of the second season of Stargate: Atlantis.

Synopsis
Atlantis is saved in the nick of time by the Daedalus, who manages to destroy the other two Hive Ships. However, 12 more are on their way, and they quickly adapt to the Tau'ri's measures. Meanwhile, the team find Lt. Aiden Ford, who has an overdose of the Wraith enzyme.

Previously on Stargate: Atlantis
Teyla Emmagan discovered that she had some Wraith DNA in her system, and with this, was able to have the ability to sense the Wraith coming and to connect with them telepathically. Stargate Command sends Colonel Dillon Everett and a team of Marines to defend Atlantis until the Daedalus arrives with a Zero Point Module. The Hive ships arrive and send several waves of Wraith Darts and beam into the city. Major John Sheppard flies a suicide mission in a cloaked Puddle Jumper. Everett is fed on by a Wraith, Dr. Elizabeth Weir looses contact with Teyla Emmagan and Lt. Aiden Ford is surrounded Wraith.

Plot
The Atlantis expedition is now faced with the monumental task of destroying the remaining two Wraith Hive Ships. Lt. Aiden Ford and his team engage with the Wraith and as a result, both groups wipe each other out leaving Ford and a Wraith soldier as survivors. Surprising Ford with an attack from behind, the Wraith begins feeding on him until a near comatose marine detonates his grenades, the consequent blast hurling Ford and the Wraith into ocean.

Major John Sheppard's brave attempt at a suicide mission succeeds; the Hive suffers fatal damage after the blast from the Genii A-bomb. Much to the relief of everyone in the city, the Daedalus has finally reached the city, and successfully rescues Sheppard by bringing him aboard. The ship's commander, Colonel Steven Caldwell, then sends two soldiers down to Atlantis to deliver the Zero Point Module to Dr. Rodney McKay, which was acquired by SG-1. ("Moebius, Part 2") McKay is ordered to install the module, but on his way to the ZPM station, the two marines are taken out by a Wraith. As he hopelessly defends himself, he is saved by Teyla Emmagan.

Meanwhile the Daedalus joins the battle with the Wraith. The ship struggles at first to destroy the second Hive ship, since the nuclear missiles they fire at the ship are intercepted by Wraith Darts miles before reaching the target. Sheppard suggests targeting the Dart Bay using the Asgard transporters to dump the weapon straight into the ship. After persuading Hermiod (the Asgard engineer on board) to override the very safeties in the targeting system that prevents this, they beam a nuke into the ship, which is quickly destroyed. The Wraith cruisers and support vessels jump into hyperspace before the Daedalus can engage them, but the remaining Wraith darts attempt a suicide attack run on the city. The attack is stopped only moments before impact by Atlantis' shield, which McKay and Dr. Radek Zelenka were able to power up with the ZPM.

With a few hours of calm, the city and surrounding areas are searched for survivors. Ford, who was thrown into the ocean, is recovered by the Daedalus and beamed down to the city. To Dr. Carson Beckett's horror, a Wraith still appears to be feeding off him when they rematerialize, but the alien is dead. Ford is alive and out cold, but the Wraith enzyme that strengthens hosts during feeding has been seeping into his system.

The destruction of the Hive ships does not fully succeed in fending off the Wraith, as the escaped cruisers have called in backup. 12 more Hive ships are en route to Atlantis. On Atlantis, the command crew struggles between what to do about the Wraith, and how to deal with Ford, who is now addicted to a wraith enzyme which makes him stronger, but also make him paranoid. Although he wants to convince his friends that he is OK he reacts very violently towards Beckett when the Doctor wants him to come back to the infirmary.

Sheppard suggests a preemptive strike against the new aggressors, which Caldwell agrees with. The Daedalus jumps to the Wraith's rest position and, using the same tactic as earlier, they successfully take out 2 Hive ships using the beams and nuclear warheads. Surprisingly, the Wraith then develop a countermeasure to the beaming technology, somehow blocking the Asgard transporters from materializing objects within the enemy ships. Unable to destroy the remaining Hive ships, the Daedalus disengages and returns to Atlantis suffering moderate but repairable damage in the process. They arrive back with only minutes to spare before the Hive ships enter the system. Caldwell sets the ship down on one of the city's piers, protected by the shield, to effect repairs to the damaged ship.

Once in orbit, the Hive ships begin a full scale orbital bombardment on the Atlantis shield. Such a drain means that their new ZPM will be depleted in a matter of days. With the Asgard transporters countered somehow by the Wraith, it is likely the Daedalus re-engaging would result in another defeat (given the odds of ten Hive Ships and dozens of Cruisers against the single ship) which would leave Atlantis unable to strike back at the Wraith. The command crew comes up with a plan to make them think the city has been destroyed by self-destruct; by linking a cloaking generator from one of the Puddle Jumpers to the city's shield, they can make the entire city disappear. To make it look realistic, they plan to use the Daedalus to transport a nuke just above the shield to make it look like a self-destruct has taken place with the thermal pulse and blast wave blocking their sensors for just enough time, before switching the shield for the cloak, vanishing the city in a massive explosion. To further convince the Wraith that they are honest with their plan, Teyla will contact them through her telepathic link and plant a defiant thought; that the people on Atlantis are going to destroy the city rather than let the Wraith get their hands on it. As a precaution, the Daedalus loads up all non essential personnel. If the Wraith don't fall for the ruse, they will run the blockade followed by the last of the Atlantis personnel in cloaked Jumpers to the second planet in the system capable of supporting life. At which point the Jumpers and their self-contained life support (otherwise there would not be enough air for a long Daedalus trip back to Earth) will meet and leave the Galaxy.

Meanwhile, Ford has gone insane. He attacks his guard in the infirmary, steals the remaining enzyme (he even threatens to shoot a wounded person in the infirmary) and commandeers a Puddle Jumper from Zelenka as the plan to fake a self-destruct is put into action, appearing at first to fool the Wraith. Using the Jumper's DHD, Ford dials an address, ignores Sheppard and escapes through the Stargate. Weir is shocked by Ford's actions, but relieved that the energy surge from the gate wasn't detected by the Hives before they break orbit, convinced Atlantis was destroyed and the gateway to Earth is no longer available.

Notable Quotes
(After Atlantis receives a transmission from Sheppard, who they believe to be dead)

Sheppard: (over radio) Atlantis base, this is Sheppard.

Weir: (in disbelief) John?

Sheppard: What other Sheppards do you know?

(Two Marines beam down into Atlantis with a ZPM)

Beckett: (jumps) How did they do that?!

McKay: (upon seeing his military escort, comprised of only two men) Whoa, whoa. This is my security escort?

Weir: Well, we are spread a little bit thin right now.

McKay: Okay. But you need to remember, if we come under fire, you have to put your lives on the line to protect me.

Weir: Rodney!

McKay: Okay, I mean, for the Zed-PM. You need to protect the Zed-PM at all costs. (pause) And me.

McKay: (Is confronted by a Wraith) So.. this is how its gonna be huh? Just me? (another Wraith enters the room) Okay, that's fine! (draws his gun) You want some of this? Huh? Huh? (attempts to fire but drops the clip instead; stares at the gun in horror) This is McKay! I'm in trouble down here! (Teyla shoots the Wraith and rescues McKay)

Weir: Rodney, we need the shield up in 40 seconds or we're dead!

McKay: What are you kidding me?!

Weir: No.

McKay: Okay, because I can't help but think you're trying determine the point at which I will completely snap. (puts the ZPM in the slot) That should do it. Fire it up.

Weir: That didn't do it.

McKay: What?!

Teyla: It is not working.

McKay: I know what she said.

Weir: 20 seconds.

McKay: Okay, SNAP! That's it. You all happy now?!

Weir: Rodney!

Weir: Rodney, you can take the rest of the day off.

McKay: Oh. I am gonna curl up in bed with the largest sandwich I can find. (lays down on the floor like he's going to go to sleep)

Teyla: Shall I just explain to the rest of the Wraith left on the base that you are unavailable to fight?

Sheppard: (is beamed to the gateroom from the Daedelaus) Hello, I'm home! (Weir hugs him, Sheppard is stunned)

Weir: Yes you are. (pause) I truly thought that-

Sheppard: Yeah, yeah, I thought the same about you for a while there. We have to stop that (referring to the fact that each thought the other had perished)

Weir: (smiling) I'd like that.

Sheppard: Look, I'm not asking you swim out there! I'm asking you to push a few damned buttons!

McKay: It's almost pretty, isn't it? (as the shield lights up under bombardment)

Weir: Ok, what are our options?

McKay: Let me see, we've got quick death, slow death, painful death, cold, lonely death...

Caldwell: Can we submerge the city again?

McKay: It's a city, not a yo-yo.

Weir: How much time do you need?

Zelenka: A week.

McKay: A couple of hours.

Weir: I'll take the second estimate.

McKay: What? Are you in a union?

McKay: (whispering) I don't think they've detected us (referring to the Wraith who are scanning for Atlantis debris).

Weir: (whispering) Why are you whispering?

McKay: (whispering) I don't know, it just seemed like the right thing to do.

Goofs

 * When the Daedalus is being fired upon, one can see the reflection of the spotlights mimicking the weapons fire on the ship behind Colonel Steven Caldwell's chair on the bridge. This is noted in the audio commentary, and future battles on Daedalus-class ships are staged to avoid this.
 * When they launch the Nuclear warhead to trick the Wraith into believing that Atlantis is destroyed, they shut down all the computers to prevent the Electromagnetic pulse discharge from damaging them. To actually prevent damage they would need to be completely turned off, but Dr. Rodney McKay opens his and immediately reacts, as though data is already on the screen. No computers boot that fast.
 * When Dr. Carson Beckett runs up to tell Major John Sheppard, Dr. Elizabeth Weir, and Teyla Emmagan that Lt. Aiden Ford has escaped, there is a yellow mark visible on the ground at Weir's feet. This is a mark to tell the actors where to stop in a scene.
 * When McKay "accidentally" ejects his M9 pistol's magazine during his uncharacteristic flash of bravery in the confrontation with the Wraith warrior, David Hewlett can be visibly seen adjusting his grip to push the magazine release, something moderately difficult though not impossible to do with a proper firing grip.
 * When Colonel Dillon Everett is emptying his M9 pistol into the Wraith attacking him, it neither cycles nor ejects shells, showing it to be either a flashpaper mockup or an empty prop with muzzle flashes added in post-production, likely for safety reasons since the actor playing the Wraith was so close.
 * When Lt. Aiden Ford was escaping Atlantis, the Atlanteans could have simply raised the stargate shield to prevent the jumper from going through.
 * It is possible that an outgoing wormhole negates this function.

Characters

 * Colonel Steven Caldwell
 * Hermiod
 * Captain Dave Kleinman
 * Captain Pat Meyers