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Known as Atlantus in Ancient language, Atlantis is a giant city-ship roughly the surface of Manhattan, which served as a capital for Ancients both in Milky Way and Pegasus galaxy. It was the stories of this city which inspired Plato to write his famous dialogue.
Located in Pegasus for the last several million years, it was recently discovered by Modern Humans, who used it as a base of operations in Pegasus for several years. Atlantis was recently brought back to Earth to fight off a Wraith threat.

History

Atlantis on Earth millions of years ago
Atlantis was created by the Ancients millions of years ago, with the purpose of being their capital. It was originally situated on Earth, on the Antarctica continent, where it stood for possibly millions of years. After a plague decimated their population somewhere between five to ten million years ago, the Ancients decided to abandon Milky Way and use Atlantis (and possibly other city ships) to travel to Pegasus Galaxy. A small Ancient outpost containing a Stargate is left in the place where Atlantis once stood, the only remnant of Ancient presence on Earth.
In the Pegasus galaxy Atlantis landed in the ocean of a planet they named Lantea, and henceforth the Ancients called themselves Lanteans. For millions of years they flourished there. Like in the Milky Way, they seeded human life and created another Stargate network throughout the galaxy. However, humans settled on an unknown world where they made contact with an indigineous life forms which started to feed on them. These creatures, named the Iratus bug, evolved with the humans until they became the Wraith. The Lanteans attempted to coexist with the Wratih, but the Wraith considered them and humans nothing more than food, and made war on them. Though the Ancients were wastly superior to them, they were unprepared for a war on that scale, and soon the sheer numbers of the Wraith began to overwhelm them. After a long war, only Atlantis, protected by its powerful shields,  remained out of all the Ancient colonies in Pegasus. The Lanteans, seeing that the war is lost, decided to hide Atlantis on the bottom of the Ocean, and retreat through the stargate back to Earth.
Atlantis remained on the bottom of the ocean for 10,000 years, and the tales brought back by the ancients eventually gave rise to the legends of Atlantis on Earth. Though unlike the legends, Atlantis was not destroyed by the ocean, it was rather a calculated descent to the bottom.
In 2004, Dr. Daniel Jackson of the Tau'ri manages to uncover the location of Atlantis and it Stargate Address. Earth promptly sends an international expedition, under the command of Elizabeth Weir, to the Ancient City. However, this completely drains their Zero point module, leaving them unable to dial out to Atlantis again. Once the team arrives, they find out that Atlantis' power source is failing, and that it will not be able to sustain its shields for much longer. While they race to find a solution to their problem, the power runs out. But rather than the city being destroyed, Atlantis simply rises from the sea bed and majestically re-surfaces before the shields fail. With no power to return to Earth and Earth unable to reach them, the expedition now must fend for themselves in an unknown galaxy.
Soon enough the expedition made contact with the Wraith, putting them and the city in danger once again.
Daedalus lands in Atlantis
In 2005 the Wraith found out the location of the city and launched a massive attack force of fifteen hive ships on it. Seeing no way to destroy them, the expedition uses a nuclear device to fake Atlantis' destruction, causing the Wraith to retreat.  For the next few years, keeping Atlantis' survival a secret becomes top priority.
At the same time, Earth, using another ZPM, manages to dial in Atlantis and send in supplies and reinforcements. They are also able to use the Starship Daedalus, upgraded with Asgard hyperdrive, to serve as a link between Earth and Atlantis.
In 2006 Atlantis is reclaimed by a group of surviving Lanteans, expelling the expedition. However, Lanteans are soon killed by the Asurans, old creations of the Ancients which turned against them, and which the expedition encountered previously. Earth is able to send forces to destroy the Asurans and reclaim the city, finding three fully charged ZPMs in the process.
Asurans once again attack the city through a satellite particle beam. with no other way out, the Tau'ri power the city's stardrive and flee from the planet. Atlantis is damaged in the process of escape and the expedition is forced to steal another ZPM from the Asurans in order to reach their new homeworld, a distant planet knwon only as M35-117.
This operation causes the loss of Doctor Weir to the Asurans, who is replaced by Col Samantha Carter. Carter is recalled back to Earth the following year, with Richard Wolsey appointed as the new commander.
Atlantis back on Earth

In 2009, the Atlantis expedition discovers that a rogue Wraith hive ship has been retrofitted with inter-galactic hyperdrive, and has made it's way towards Earth. With Earth's ships powerless against it, Atlantis was once again powered up and made its way back to its ancient home. In the battle Earth's defenses were able to destroy the Wraith ships, but not before it forced Atlantis to crash land on the planet. Atlantis landed on the ocean near San Francisco, but managed to activate its cloak just in time, leaving the population of Earth none the wiser.

Layout

Atlantis is arguably the greatest single artificial structure in the Stargate Universe. It is a snowflake shaped city-ship with roughly the surface area of Manhattan. The control room and the stargate are housed in the central spire located in the middle of the city. Many other buildings are spread throughout the surface of the city. On the underside, massive engines provide lift and space travel capabilities. Rapid access through the city is provided by a network of teleporters.

Technology

Atlantis was created by the Ancients, and as such is among the most advanced structures/ships known to man. The city is far from fully explored by the Tau'ri, and new technologies are found every day.

Defense
Shields

For defense Atlantis boasts the most powerful shields ever created by the Ancients. The shields are completely impenetrable, so long as enough power is supplied to them. They were able to hold back the pressure of the ocean for ten thousand years, and are able to withstand days under full bombardment by the Wraith.
Atlantis also has a complement of Ancient drone weapons. At its hayday there were likely tens of thousands of drones housed in Atlantis, but when the Tau'ri arrived, only a few dozen of them remained. The expedition later managed to replenish the stock.
Other defense means were also mentioned, but none were seen so far.

Power

ZPM room
Atlantis is powered primarily through Zero Point Modules. the city requires three ZPM's to function at full capacity, though a single can provide power for the most basic systems. It can also be powered by several Naquadah generators, albeit at a far lower functionality. On Lantea Atlantis was also powered by a geothermal drilling station.

Propulsion

Atlantis' stardrive allows the city to achieve orbit and travel between galaxies via hyperspace. To protect its inhabitants during flight, the city is equipped with inertial dampeners.The power requirements of the stardrive are enormous. While fleeing from the Asurans, the Atlantis Expedition is able to launch the city with a single ZPM by adding additional power from an Ancient geothermal drilling station during the first few minutes of lift-off. However, Atlantis runs low on power before it reaches its intended destination, due to damage to the power distribution system. 30% of the total power requirements are consumed within the first few seconds of flight. In "Enemy at the Gate", Atlantis uses a dangerous and experimental wormhole drive to travel to Earth nearly instantaneously.

Transportation
Atlantis stargate

For transportation around the city, Atlantis houses a network of transporters, which are presumably successors of the ring transporters seen in the Milky Way.
For travel outside of the city, there is a fleet of Gateships, small vessel which can travel through space, but also pass through a stargate.
The stargate is housed in the command room, atop the central spire. This room presumably once housed the Antarctica gate found on Earth.

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