Second Siege of Atlantis
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The Second Siege of Atlantis was a ferocious battle that took place in mid-2005, between Wraith forces assaulting the Lantean city of Atlantis, and the Human Atlantis expedition occupying it. It was the first time the city had been attacked by the Wraith since the end of the Lantean-Wraith War 10,000 years prior.
The Atlantis expedition arrived in the city a number of months prior to the battle, and their actions in those first days precipitated the massive assault that would come later. Having found the city still submerged beneath the ocean of Lantea, a team led by Col. Marshall Sumner was sent to find a potential evacuation site should the city's shield fail. The mission was to a world later learned to be Athos, where they made first contact with the Athosians.
While in the Athosian camp, a Wraith Dart came through the Stargate and began culling the local population. In the process, a number of influential people–including Col. Sumner–were taken captive. A rescue mission was mounted by the military contingent's acting commander, Maj. John Sheppard, but they did not realize that the Wraith vessel they had boarded was one maintained by a Keeper. Sheppard was unable to reach Sumner before the Keeper interrogated and fed upon him, and chose to euthanize his superior in an act of mercy. Sheppard later also killed the Keeper, inadvertently triggering the awakening of all the hibernating Wraith, galaxy-wide.
In just a few months short of a year since their arrival, while searching for Zero Point Modules to power the city, the expedition had an unexpected encounter: a Dart, a short-range one-man vessel, was rapidly approaching the city. It was able to buzz the city several times before being destroyed, apparently scanning and taking readings of the city before sending a transmission. By restoring Atlantis' long-range sensors, the expedition discovered that three Hive ships were on a direct course to the unprotected city–the Wraith attack that they knew was inevitable was now just two weeks away. (ATL: "The Brotherhood")
The time was not wasted. A reconnaissance mission consisting of Maj. John Sheppard and Teyla Emmagan traveled to a world on the path of the Wraith armada to determine its strength, where they determined that each Hive ship functions as the heart of its own carrier group, with a number of Cruisers and countless Darts escorting each. The armada was stopping at various worlds on their way to Atlantis to feed, meaning that the Wraith would be at their fullest strength by the time they arrived. Meanwhile in Atlantis, Dr. McKay devised a means of data compression which allowed them to dial Earth and transmit a data burst consisting of all that they'd learned since arriving in Pegasus. This would later prove to be a key factor in the defense of the city. (ATL: "Letters from Pegasus")
Shortly after returning to Atlantis, Emmagan began having nightmares of a Wraith in the city feeding upon her. While initially thought to be a result of stress, it was later determined to be much more than that. She, along with Dr. Carson Beckett, learned that at some point in the past, a Wraith had manipulated the genetic structure of her ancestors. This had manifested itself all her life as being able to sense the Wraith's presence before they attacked, but now it had become of much more immediate use. It was determined that she could, in fact, interact with the Wraith psychic network and even see through the eyes of some of the ones on the ships headed toward Atlantis.
Using this as a means of intelligence-gathering, they were able to determine the true objective of the Wraith attack. Instead of simply planning to destroy the city, the Wraith were planning to seize it for their own. The Atlantis Stargate was the only gate in Pegasus capable of dialing back to Earth, and the Wraith themselves did not possess intergalactic hyperdrive such as the one powering Atlantis. Capturing either would allow them to assault Earth in force. The defense of the city had just become even more important. (ATL: "The Gift")
With the Wraith fleet fast approaching, a plan was devised to attempt to repair the Lantean Defense satellite which had been discovered a few months previous. While at some point there had been dozens of these units scattered throughout the Lantean system, only one had been rediscovered and it happened to be in the path of the approaching Wraith, so it was a perfect opportunity. A repair team consisting Lt. Miller and Drs. Grodin and McKay rushed to repair it before the arrival of the Wraith fleet. Finding it damaged made this a challenge, but they were able to successfully reactivate and power up the defense satellite, which promptly and handily destroyed one the Hive ships. Unfortunately this also overloaded the power systems, and the surviving Wraith ships easily destroyed the satellite–with Dr. Grodin still on board.
With their only line of defense destroyed and Wraith victory seemingly inevitable, expedition leader Dr. Elizabeth Weir ordered that both the city self-destruct system and a virus devised by Dr. Radek Zelenka to erase the Atlantis Database be put on standby mode, to be activated when and if defeat became inevitable. (ATL: "The Siege, Part 1")
As the expedition prepared to retreat, they were faced with an unexpected development. An incoming wormhole connected–from Earth. Dr. McKay's data burst had been a complete success and their transmission received. Now, an entire contingent of military reinforcements with all manner of defensive equipment poured through the gate. Commanded by Col. Dillon Everett, soldier after soldier carrying crates of supplies arrived in the city of the Lanteans. But Everett revealed the greatest surprise to Weir himself: Earth's newest battlecruiser, the Daedalus, was mere days away and was carrying a fully-powered Zero Point Module. The successful defense of the city now hinged on holding the line till the Daedalus arrived.
Col. Everett immediately took charge of preparing the city's defenses. He ordered the deployment of railgun weapons platforms in strategic locations to defend against incoming Darts, took personal charge of prioritizing the scientific team's assignments, and ordered the new Mark II naquadah generator interfaced with the control chair so that Atlantis' armament of drone weapons could be employed in their defense. He also ordered the strategic placement of proximity-activated thermonuclear devices in orbit above the city, effectively laying a minefield for the Wraith fleet to fly into. (ATL: "The Siege, Part 2")
The siege begins
Whether more intelligent than the expedition gave them credit for, or if they simply possessed superior sensors than had been assumed, the Wraith did not fall for the minefield trap. Instead they launched ahead of their armada a wave of captured meteors to trigger the devices' proximity sensors. The tactic worked perfectly for the Wraith, eliminating the minefield in addition to temporarily blinding Atlantis' sensors. Some of the meteorites rained down on the city, but most were destroyed in the blasts.
The sensor blindness was a tactical advantage that the Wraith immediately took advantage of, launching an enormous wave of Darts to assault the city and soften up their defenses. The spectacular battle saw countless railgun positions blasting into the night sky, destroying many Darts while they in turn rained their own destruction on the unshielded city. As the various groups of soldiers manned their stations, Maj. Sheppard activated the control chair to bring the drone weapon system online. Though it only had a few dozen left, he was able to assist by shooting down a number of Darts. Eventually the last of the Darts was destroyed and they had survived the first wave. But two Hive ships, Cruisers, and many Darts still lay in wait in orbit.
With the city's sensors still inoperable and the supply of drones exhausted, Col. Everett was open to suggestions as to how to proceed next. Drs. McKay and Zelenka and Maj. Sheppard simultaneously arrived on the idea of remote-piloting cloaked Puddle Jumpers loaded with explosives right into the Wraith ships and detonating them, destroying the enemy from within. The problem of not having any more nuclear weapons, due to the asteroid attack, had a unique solution.
Dr. Weir offered to use her expertise in negotiations to contact the hostile Genii, who possessed their own nuclear weapons development program. Making contact, she was initially taken as a captive before they agreed to the generous terms offered by the expedition: large supplies of C4 explosives in exchange for the Genii prototype nuclear weapons; the Genii would be able to see how well their experiment worked at no risk to themselves.
She returned to the city with the devices and they were immediately loaded into the Jumpers, but by then a new problem had arisen. Another wave of Wraith ships were on rapid approach, and Wraith soldiers were already in the city, while the naquadah generator powering the control chair was depleted. There was no way to remote-pilot the Jumpers. Unable to contact Col. Everett, who was engaged in fierce personal combat with Wraith soldiers, Maj. Sheppard made the dire decision to personally pilot one of the nuclear-loaded Jumpers on a suicide attack. (ATL: "The Siege, Part 2")
As Maj. Sheppard's cloaked Jumper drew closer to the Hive ship's docking bay, he resigned himself to his fate and prepared to meet his end. With just moments to spare, he received a transmission from Col. Steven Caldwell, commanding officer of the just-arrived Daedalus. Sheppard was transported aboard and the Jumper left to make its final voyage. Seconds later, it detonated inside the Hive ship, vaporizing it completely. Taking advantage of the respite, Caldwell ordered that the Zero Point Module they were carrying be transported down to the city immediately so it could be installed.
The Daedalus then engaged the Wraith forces directly, drawing them away from attacking the city below. Using conventional weapons such as mounted railguns and missile-propelled nuclear weapons, they were unable to destroy the large Wraith vessels so a new strategy was devised. With the aid of Asgard advisor Hermiod, the transporter system was re-purposed to materialize another nuclear weapon deep inside the final surviving Hive ship. There it detonated, leaving only a few Cruisers and Darts surviving.
The Cruisers turned away and jumped to hyperspace, but the Darts orchestrated one final assault. Lining up along a similar trajectory, all the surviving Darts turned back to the planet and launched a kamikaze attack. Dozens of Darts flying at maximum velocity, accelerated by the natural pull of Lantea's gravity barreled at the city, aiming to destroy it utterly. Fortunately for the expedition's sake, Dr. McKay was able to install the ZPM and raise the city shield in time to prevent disaster. The Darts exploded spectacularly, but could not penetrate the defensive barrier.
With the last of the Wraith presence defeated, it appeared that the siege was ended. When Atlantis' long-range sensors finally came back on, it was discovered instead that it was only a pause; another wave of 12 Hive ships was on its way. Resolving to confront the threat before it reached their doorstep again, Col. Caldwell and the Daedalus immediately departed with the intent of continuing to exercise the tactic of beaming warheads inside the Hives.
This counter-offensive was initially a success, as the Daedalus was able to destroy two more Hive ships without incident. But the Wraith learned from the tactic and devised a means of jamming the inbound transport, effectively blocking the Daedalus' attacks. Outnumbered and massively outgunned, Caldwell ordered a retreat back to Atlantis and sought refuge for the damaged ship inside the city shield. (ATL: "The Siege, Part 3")
The massive Wraith fleet arrived over Atlantis as expected, and immediately began orbital bombardment of the city shield. While the shield could theoretically run indefinitely, the sustained bombardment was causing significant drain of the city's lone ZPM and was likely to fail in a matter of days. Once more facing a desperate situation, the expedition leaders devised a perilous plan. The cloaking device from a Puddle Jumper could be disconnected and interfaced with Atlantis itself, rendering the entire city invisible both to sensors and the naked eye. But this meant redirecting shield power through the cloak, which would leave the city defenseless.
So the group decided to employ Teyla Emmagan's recently-discovered Wraith telepathic ability to their advantage again. A seed was planted in the Wraith telepathic network indicating that the expedition was planning to destroy the city utterly in order to prevent Wraith capture. The Wraith fleet paused their attack to observe, and in that moment the expedition acted. One of Daedalus' nuclear weapons was transported to a point in mid-air above the city shield and detonated, blinding the Wraith sensors to anything beneath. When Dr. McKay was satisfied that the radiation levels were no longer fatal, he deactivated the city shield and transferred the power through the cloaking device, hiding the city.