The Second Siege of Atlantis
A second attack by the Wraith on the city of Atlantis, drawn out over a period of several days, and the first faced by the Atlantis expedition from Earth. (The First Siege of Atlantis took place some 10,000 years earlier, when the Ancients still occupied the city.) Originally three Wraith hive ships were detected, but that number would escalate after the city received aid from Earth.
The battle would end with an ingenious plan that could conceivably prevent the Wraith from ever returning ...
A single Wraith Dart arrives in the city and begins scanning its structures. Dr. Elizabeth Weir orders the population confined to their quarters. Puddle Jumpers are deployed to deal with the threat and one is destroyed, killing officers Markham and Smith. After it completes its scans the Dart transmits a message into deep space and self-destructs -- but, unbeknownst to the expedition team, the pilot is beamed safely into the city. Dr. Zelenka scans that region and locates three Wraith hive ships. If they maintain course and speed they will be over the planet in two weeks.
Zelenka calculates at least three hyperspace "pit stops" the hive ships must use, either because their hyperdrive technology is limited or they must gather food to sustain their journey. John Sheppard and Teyla Emmagan fly a Puddle Jumper through a nearby planet's Stargate to gather intelligence on the threat. When they arrive they are forced to witness the culling of that world, but the Jumper is able to save a few inhabitants before returning to Atlantis.
Realizing Teyla is able to communicate with the Wraith's telepathic network, Dr. Heightmeyer instructs her to think back to the time when she and her father were captured. But during two of the sessions a Wraith manages to take control of her instead, to deliver a message: "Nothing can stop us." But she is able to ascertain that the Wraith are more interested in getting to Earth than taking Atlantis. Meanwhile, the Atlantis Alpha Site's location is discovered by the Wraith.
With hive ships in range of the Atlantis system in 49 hours, Dr. McKay deduces their last hyperdrive stop will be in range of the last remaining Ancient defense satellite at the far end of the solar system. Because its power cells have been depleted for 10,000 years they won't see it as a threat, but a single naquadah generator can at least partially charge the weapon, which when powered should be able to destroy the ships. McKay, Dr. Grodin, and Miller are sent to reconfigure the satellite. After one successful shot the rerouted circuit pathway fries. The two remaining hive ships and their escorts destroy the satellite (with Grodin aboard), but they also briefly halt their approach to rethink their strategy.
Before the hive ships reach orbit they send out multiple squadrons of Darts to attack the city at night. At this point, reinforcements have arrived through the Stargate from Earth, including multiple troops with advanced rail gun weaponry. A command chair in the city is manned by Major Sheppard, who launches the remaining Ancient drone weapons against the attackers to fight off the ships.
Dr. Weir travels to the Genii homeworld to meet with Prenum, hoping to negotiate for some of their weapons. Meanwhile troops are deployed throughout Atlantis to eliminate Wraith soldiers that were beamed down via the darts. Drs. McKay, Zelenka, and Beckett use the command chair to try and automate Puddle Jumpers so that the Genii weapons can be placed within them and sent into the bellies of the hive ships without the loss of pilots.
When the hive ships enter orbit they release a second wave of darts that rain down upon the city. The command chair is not allowing Sheppard to interface with the Jumper remotely, so he is forced to take the Jumper into the hive ship himself, armed with one of the Genii nuclear warheads.
Just before Major Sheppard sacrifices himself he is told to de-cloak the Jumper and Asgard beams transport him aboard the Earth battlecruiser Daedalus, which has finally arrived. The Jumper detonates, taking out the second hive ship. Colonel Caldwell, commander of the Daedalus, orders the Z.P.M. beamed to Atlantis. Using the Asgard beams to transport nuclear weapons into the hive ships, the last carrier is successfully destroyed. The Wraith cruisers escape into hyperspace and all remaining darts make a kamikaze run. Fortunately the Z.P.M. is connected and powers the city shield.
With deep-space sensors returned, 12 more hive ships are detected. The Daedalus is sent to stop them at their next hyperspace stop, and the Asgard beams are successful at depositing warheads inside of two of the ships before the Wraith engage countermeasures preventing any more. With ten vessels remaining and no way to win the fight the Daedalus returns to Atlantis.
The Daedalus returns to Atlantis in time to land on the East pier just before the ten remaining ships arrive, pelting the city with energy weapons fire. With the intensity of the hits the Z.P.M. will only maintain the shield for a matter of days. The senior staff gathers in the situation room to come up with a plan and realize that if the Wraith thought that Atlantis was destroyed, there would be no reason to remain. The coordinates to Earth would be lost and they would depart.
Teyla links telepathically with the Wraith to greater affirm this ploy. Surprised at the sudden change in strategy, and not wishing to aid the Atlanteans by destroying the city they are attempting to access, they cease fire. The Daedalus drops a nuclear warhead just above the city's shield, which detonates, and Atlantis switches from the shield to a Puddle Jumper's integrated stealth device, cloaking the city-ship.
The ploy works. Believing Atlantis has been destroyed, the hive ships and their escorts depart. Preliminary accounts estimate the casualties at 40 losses, perhaps more. The injured are sent through the Stargate to Earth, and with the threat long-gone, Atlantis de-cloaks again.
The Brotherhood - With long-range sensors online, Dr. Zelenka discovers that three Wraith hive ships are on the way to Atlantis.
Letters From Pegasus - Atlantis's possible destruction imminent, the expedition team records messages for a quick Stargate wormhole burst to home.
The Gift - Attempting to gain intelligence on the incoming assault, Teyla interfaces with the Wraith telepathic consciousness.
The Siege, Part 1 - Atlantis sends out a Puddle Jumper to recharge the Ancient defense satellite. It successfully destroys one of the hive ships before being annihilated.
The Siege, Part 2 - The hive ships enter planetary orbit and send out two waves of Wraith darts against the city.
The Siege, Part 3 - The Daedalus arrives to destroy the first wave -- and three more hive ships -- and eventually launches a nuclear warhead above the Atlantis shields, making the Wraith believe the city has been destroyed.