The Siege, Part 3

"The Siege, Part 3" is the season two premiere of Stargate Atlantis.

Plot
The Atlantian task force is now faced with the monumental task of destroying the remaining two Wraith Hive-Ships. Major Sheppard's brave attempt at a suicide mission succeeds; the Hive suffers fatal damage after the blast from the nuclear device. Much to the relief of everyone in the city, the Daedalus has finally reached the city, and successfully rescues Sheppard by beaming him aboard. The ship's commander, Col. Steven Caldwell, then sends two soldiers down to Atlantis to deliver the ZPM to Dr. McKay, which SG-1 acquired in season 8 (see "Moebius"). 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.

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 beaming technology 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 prevent this, they teleport a nuke into the ship, which is quickly destroyed. The 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 the Atlantis shield, which McKay and Zelenka were able to power up after a few problems 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 during Part II, is recovered by the Daedalus and beamed down to the city. To 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 Aiden 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 Dr. Beckett when the Doctor wants him to come back to the infirmary.

Major 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 materialising 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 doesn’t fall for the ruse, they will run the blockade followed by the last of the Atlantis personnel in cloaked puddle jumpers to the planet from 'Defiant One' in the system. 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.