Atlantis was built millions of years ago by the Ancients. The city resided in Antarctica on Earth until five to ten million years ago, when a deadly plague prompted the Ancients to relocate it to the Pegasus galaxy. There, it served as the Ancients' capital as they built a new system of Stargates and seeded many worlds with humans. However, the Ancients' activities gave rise to a powerful new species, the Wraith. With their vastly superior numbers, the Wraith drove the Ancients from their holdings until only Atlantis was left, defended by its powerful shield and a network of armed satellites. The Wraith laid siege to Atlantis for one hundred years until the Ancients, unable to see a path to victory, submerged the city and returned to Earth through the Stargate. There they merged with the native human population, and their accounts of Atlantis gave rise to the classical myth of the Lost City. Atlantis itself lay on the ocean floor, empty and dormant, for ten thousand years.
The Lost City of the Ancients is first mentioned by Daniel Jackson in the season 6 finale of Stargate SG-1, "Full Circle". In the episode, he directs SG-1 to a tablet that mentions the Lost City, and tells them that there are powerful weapons there capable of defeating Anubis. The search for the Lost City continues through season 7 of SG-1, and although the team finds the Ancient outpost in Antarctica, the location of Atlantis itself remains a mystery. In the Stargate Atlantis premiere "Rising", Jackson discovers that the Stargate address to Atlantis contains eight symbols, meaning that it is in another galaxy. The multi-national Atlantis Expedition, led by Dr. Elizabeth Weir, is formed to investigate the city, with the knowledge that they might be unable to return as they cannot bring Earth's sole ZPM with them.
The Expedition arrives on the planet Lantea (ATL-984) to find Atlantis still underwater. With power nearly exhausted, a failsafe releases the city and it rises to the surface. The episode "Before I Sleep" reveals that the expedition actually arrived at Atlantis twice, the first time in an alternate timeline. The first time, there was no failsafe and most of the personnel drowned. Weir, the only survivor, travels back 10,000 years in a puddle jumper she found fitted with a time machine. There, she changes the timeline by convincing the Ancient Janus to help her ensure the survival of the city and her people.
Atlantis is cut off from Earth for most of the first season, and must face an impending Wraith attack alone. In the season 1 finale "The Siege, Part 2", Earth reestablishes contact with Atlantis using a ZPM recovered from Egypt (detailed in the SG-1 episode "Moebius"), and sends supplies and reinforcements. The Earth ship Daedalus subsequently brings the ZPM to Atlantis in "The Siege, Part 3", but Atlantis only survives the Wraith attack by pretending to destroy the city while instead rendering it invisible. Keeping the continued existence of Atlantis secret from the Wraith thus becomes a top priority in the following seasons. The Daedalus, newly fitted with an intergalactic hyperdrive, then provides a regular link between Atlantis and Earth.
In season 3, Atlantis is briefly reclaimed by a group of surviving Ancients in "The Return". The city then falls to the Asurans (better known as the replicators), and is finally retaken by Earth forces. The Atlantis Expedition recovers three ZPMs from the Asurans' occupation, two of which are taken to bolster Earth's other defenses. At the end of season 3, Atlantis comes under attack by an Asuran satellite weapon. McKay and his team figures out a way to activate the city's stardrive and escape, but the city runs low on power well short of its destination. In the second episode of season 4, "Lifeline", the Atlantis team steals a ZPM from the Asuran homeworld to power the rest of their journey, and Atlantis touches down on a new world, M35-117. With Dr. Weir captured by the Asurans, Colonel Samantha Carter is appointed as the new Atlantis commander. At the beginning of season 5, Carter is recalled to Earth and the IOA appoints Richard Woolsey as the new leader of Atlantis. In the Atlantis series finale "Enemy at the Gate", Atlantis returns to Earth via a highly dangerous and experimental wormhole drive to defend it against a ZPM-powered Wraith hive ship. The city is thrown into a decaying orbit by weapons fire and lands in the Pacific Ocean near San Francisco. It is not currently known if Atlantis will remain on Earth due to the destruction of Earth's Ancient Control Chair in the Wraith attack, or if will return to the Pegasus galaxy via the Wormhole Drive or the Star Drive.
Atlantis is a huge, snowflake-shaped platform covered in skyscrapers; at the center is the central spire, the tallest building in the city. The central spire contains the main control room, referred to as Stargate Operations (also called the Gate Room), and the Stargate itself. Rapid access throughout the city is provided by a network of transporter rooms. The underside of the city contains the massive engines which propel the city through space, as well as the docking point for an Ancient outpost. The city itself is the size of Manhattan.
According to visual effects artist Bruce Woloshyn, the model of the city of Atlantis, when they first built it, was over four million polygons - feature film in size. There is thus a lot of detail that they can back up, allowing the city to look really nice, even from an extremely close view. Also, most of the city is modelled, not textured, which allows for the details to move when the city is turned around.
Many sets used for Atlantis (and also SG-1) are actually part of a massive sound stage which was built for almost two million dollars. This large stage is used for rooms like the brig, several balconies including the ones with the grounding stations or other interior parts of Atlantis. If they require outdoor views they use green screens to hide parts of the set. Also some sets of Atlantis are part of the set which was used for Blade: Trinity, for example the bridge seen first in "The Storm" or the infirmary in "Michael".Auxiliary control center: This is a large room in the underground of the city. It allows people to control the city if the main operations center is unavailable. From this room a person can, for example, use the communications system or power up the city's star drive.
Brig: Rooms equipped with cages in the middle, consisting of horizontal bars re-inforced by powerful force field, used to lock dangerous people away. The Atlantis expedition used the brigs several times to imprison captured Wraith and Genii.
Chair room: Like the Ancient outpost in Antarctica, Atlantis also contains a control chair. It is used by Sheppard to control the city's drone weapons in "The Siege". It is also used to fly Atlantis in "First Strike", "Lifeline" and "Enemy at the Gate".
Conference rooms: Atlantis houses two known conference rooms, both below the Gate room, that allows the leadership to discuss important matters. The smaller one is used for only a few people, and it contains only a large triangle-shaped table with chairs. Another bigger one, which contains a longer table, is used for large meetings in which many people can take part. Each of these rooms can be accessed by multi-panel doors.
Hologram room: A room that allows access to the Ancient database in the form of holograms. In "Rising", it plays a message from the Ancient Melia describing their history in the Pegasus galaxy. Sheppard uses the room to show Colonel Evrett the galactic tactical situation in "The Siege". In "The Pegasus Project", Daniel Jackson and Vala Mal Doran use the room to search for information about planets where the Sangraal might be hidden. The Ascended Ancient Morgan le Fay poses as the teaching hologram she originally invented in order to give them the information. The room is relatively power-intensive and so is used sparingly.
Gym: An empty room which is used by the personnel to train. This room is often used by Teyla Emmagan, John Sheppard and Ronon Dex.
Infirmaries: Atlantis has several medical facilities, (though it is unclear if the Ancients originally used them for medical purposes, or if the Atlantis expedition simply chose to use these rooms for their own needs). These rooms house many different medical devices, most of them from Earth, but some left over by the Ancients. The rooms also hold possibilities for medical and biological research. The primary medical facility is a large room meant to watch over several patients. There are additional facilities (including an adjacent room) where people can recover, as well as a single room for treating only one person while other people can watch from above through a large glass façade. The medical facilities were under the command of Dr. Carson Beckett, though after Beckett's death, he was replaced by Dr. Jennifer Keller.
Jumper bays: The main puddle jumper bay in Atlantis is a two-story facility, located atop the central tower. The jumpers can exit either outside through a portal in the roof, or into the control room to travel through the Stargate. The design of the jumper bay changes after the season 3 episode "The Return", in which Sheppard's team destroy much of the upper central spire. "The Return" also shows that there is another jumper bay accessible from the ocean underneath the city.
Laboratories: Atlantis houses a vast number of laboratories, which the Ancients used to conduct many different experiments. Over time, the Atlantis expedition stumbled upon a number of these. These laboratories have contained an energy creature, a nanite virus, a stasis capsule containing an alternate version of Elizabeth Weir, a human advancement device similar to a DNA resequencer, a zoology lab, and a device that creates explosive tumors.
Living quarters: Since Atlantis is a city designed for use by the general population, and not the military, there is presumably enough room for thousands - if not millions - of inhabitants. Some quarters are rather small, lacking much free space, and can only house one person; others are bigger and provide more room.
Mess hall: A large hall located halfway up the central spire, where Atlantis personnel can eat or socialize. It has a spectacular view of the city.
Outpost: When Atlantis resided on Earth in Antarctica, it was docked with an Ancient outpost. The outpost is powered by a ZPM and contains a shield and a large number of drone weapons. The outpost was left behind when Atlantis travelled to Pegasus. Another, similar outpost is found on Proclarush Taonas.
Stargate operations: The main control room of Atlantis, located in the central tower, contains all devices and control consoles to operate the city. Here, the DHD of Atlantis is located (and the only one which can make a connection with Earth, as it has a special control crystal to do so) as well as controls for the Stargate force field, city-wide communications, external communications, energy systems, multiple sensors, access to the Ancient database, the city's shield and much more. Later, a console (found to be a biometric sensor) is found and installed in the operations center . In the direction of the gate room, the center is enclosed with a glass façade and a balcony, which allows the people to watch the gate area. Lastly the room provides access to the Puddle Jumper bay and a balcony at the backside.
The city holds many secrets and technology far in advance of that mastered by the human expedition. In regular use are the transporters to move people and objects around the city and the Puddle Jumpers docked in Atlantis. The city has not been fully explored due to its size, and search teams are finding new rooms and technology every day.
Atlantis holds a vast database of Ancient knowledge. Even with all the hard drives the Atlantis expedition brought with them, and the use of an efficient compression codec invented by Dr. McKay, only about 9% of the translated database could be stored. The database holds a collection of Stargate addresses for both Pegasus and the Milky Way, information about the Wraith and the Iratus bug, information about other species, and much scientific research (including zero-point module research, work on ascension, weapon schematics and notes on space travel). The database also has an incredible ability to back up data, so deleting it is difficult. The database can be accessed through many database terminals in the city.
The main defense system of Atlantis is its energy shield, without which the city is surprisingly fragile. While the shield can effectively hold back almost any threat, it consumes so much power that a Zero Point Module is required to activate it. In "The Eye", McKay uses the energy of multiple lightning strikes to briefly power the shield. The Ancients once extended the city's shield over much of the hemisphere in order to protect the native life against a coronal mass ejection from the planets star. In "The Siege, Part 3", the Atlantis Expedition links the cloaking generator of a puddle jumper to the city's shield generators, converting the shield into a cloak. This is used to fool the Wraith into believing Atlantis has been destroyed, and is used in subsequent episodes to hide from the Wraith. In "The Return", the Atlantis team modifies the shield generators to emit a replicator disruptor wave.
The primary weapons of the city are drone weapons, which require the Ancient control chair to fire. At the time of "The Siege", Atlantis has only a few dozen drones left, which are all used in defending the city against the Wraith. The city's drone supply is replenished from the stores of another city ship discovered in "The Tower". The SGC also installed multiple railguns, machine guns, and SAM missile emplacements during The Siege, however, these weapons have not been featured on the show since, so it is unknown if the weapons are still fitted. Jumpers are also used in the defense of Atlantis. In Brotherhood, three Jumpers are dispatched to destroy a Wraith Dart and in Lifeline, multiple, if not all, the Jumpers are used to launch drones to clear a path in an asteroid belt for Atlantis to go through. Although it was mentioned in The Gift that the Atlantis Expedition had "uncovered a number of defensive weapons systems beyond the shield" none of these have appeared on the show to date.
Atlantis is powered by three Zero Point Modules, though most systems can function with just one installed in the Power Vault. The Atlantis Expedition has installed a series of naqahdah generators, which are sufficient for basic systems. The city also has solar power generators that can power minor systems. Power is distributed throughout the city via conduits lining the walls of every corridor. The city will automatically power up sections when people enter them, and can also make some system adjustments to compensate for low power.
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 city is flown from its Ancient control chair. The power requirements of the stardrive are enormous. In "First Strike", 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.
The city is equipped with several types of sensors: first the long-range sensors, which allow Atlantis to scan distant star systems. These sensors also enable the inhabitants to detect any ships that are on their way to the city, and thus be warned. This set of sensors ran in the background and was discovered months after the arrival of the expedition. Another set of sensors are the internal sensors, which display detailed plans of the city and life-forms in it. Although it can distinguish between organic and energy life forms, it cannot differentiate between organic life forms.
The third set of sensors are the biometric sensors that scan the city for irregularities in biometric rhythm. If people of different species are in the city, the sensors detect them. These sensors were discovered by the Atlantis expedition about one month before the arrival of the Wraith. However the biometric sensors need a lot of power so they were ordered to only scan the gate room.
The transporters are the primary means of transport to move quickly between different parts of the city. They are small chambers and if someone enters, a console opens in the back and reveals a map of the city with blue lights that display the location of the other chambers. To be transported to another chamber a user only needs to press one of the blue lights at the target location. Afterwards the people in the chamber are transported to this location in a blinding flash of light. This system functions in a similar manner as the Ring Transporters which doesn't come as a surprise since both systems were invented by the Ancients. The chambers also function as elevators to move people up and down in the same structure or building.
Atlantis experiences frequent lightning strikes; for protection there are lightning rods throughout the city, which channel the electricity to four grounding stations that lead into the ocean.