10,000 years ago, Emege was a great city on Athos protected by the Lanteans. People lived, worked and grew old there under the protection of the Lanteans. The Lanteans also gave the people of Emege great treasures and some even dwelled within the city. After the Lantean-Wraith war began, the Lanteans who dwelled in the city were forced to depart to take part in the fighting, not explaining what was going on to the Athosians who they claimed wouldn't understand.
After the Lanteans started losing the war with the Wraith, the Wraith attacked Athos with hive ships and Wraith cruisers to use the Athosians as food for the First siege of Atlantis. While the rest of Athos fell, the city had a Lantean energy shield that protected it for a year and a day, the last safe place on Athos. After that, the shield's power supply was depleted and Emege fell to the Wraith led by Queen Death. Queen Death stalked the streets of Emege and slew for the love of it, men, women and children alike while her soldiers dined on everyone so that the city wouldn't rise again. After destroying Emege, the Wraith left Athos, leaving the Athosian civilization ruined. As the Athosians tried to survive and called out to the Lanteans for help, a young man named Arda returned, released by the Wraith into the ruins of the city. Arda tells his people that Queen Death is dead, but the Lanteans are gone and will no longer be able protect them and have released him as the Wraith have no need for him anymore. Arda urges his people to rebuild a world of man without the Lanteans, comparing the situation to a parent who has left their child to fend for themselves in the greater world. (SGA: "Death Game")
Following the return of Arda and upon his urgings, the Athosians rebuilt Emege before the Wraith returned two generations later. After an unknown number of times rebuilding the city, the Athosians abandoned Emege for good after the last great holocaust of Athos approximately 500 years before the Tau'ri visited the planet. The Athosians did not go into the city, for fear of bringing the Wraith down upon them. Colonel Marshall Sumner and some of his team went to search the city while on Athos in hopes of finding a ZPM but didn't find anything useful. (SGA: "Rising", "The DVD Collection 64", "Death Game", "The Furies")
In 2009, the Wraith Commander Guide revealed to Teyla that the legendary Queen Death that destroyed Emege is in fact Coldamber, the Wraith Queen encountered by the Atlantis expedition under the ocean who was ultimately killed by Sheppard and Doctor Rodney McKay. (SGA: "The Furies")
In 2010, Teyla suggested an expedition into the city to determine if there was in fact a shield generator there in hopes of the Athosians possibly returning to their homeworld. Together, Teyla and McKay, with the help of Halling, convinced the Athosian Council to allow the two of them to explore Emege. In the ruins, McKay and Teyla located the control room and McKay was able to discern the events that truly led to the fall of the city: instead of running on a ZPM, the shield ran on geothermal power from a supervolcano in whose caldera the valley Emege sat in. Running the shield for so long continuously threatened to cause the supervolcano to become unstable and erupt. Heeding the warnings, the people of Emege chose to shut down the shield themselves, effectively sacrificing themselves and their city to preserve Athos itself and the Athosians surviving in hiding on other parts of the planet. (SGA: "The Mysteries of Emege")