Atlantis is the civilization of the Atlanteans. The inhabitants used the Time Machine to retreat far into the past to save the human race. Eventually after many attacks from the Vortex, Atlantis sunk into the ocean in an area west of the Asterite's Cave. The entire city has since become infested with sharks, jellyfish and other creatures. Atlantis is not just one city, but a civilization which incorporates several cities, such as the City of Forever.
Atlantis itself is very large and filled with many relics of highly advanced technology. However what Ecco does not encounter are any remains of weapons, meaning that they were all destroyed or exhausted in the war with the Vortex.
As Ecco makes his way through the city he encounters numerous traps and puzzles.Perhaps the Atlanteans put them there in anticipation of a ground war with the Vortex or to prevent undesirables from gaining access to the Library and Time Machine. There are stone carvings of human statues and temple-like structures spread throughout. This shows that the Atlanteans had a cultural life as well.
The two most important parts of the city are the Library and the Time Machine, which is located in the City of Forever. The Atlanteans recorded the history of their civilization and race in glyphs so that when the Singers eventually find the city, they would know what happened. The Time Machine is stored in the deepest part of Atlantis. It survived the Vortex attack and is still functional.