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Atlantis left Avalon and traveled to a galaxy untouched by the Alterra in the hopes of keeping this new seed species they were going to create away from the plague that had been randomly popping up in their inhabited 22 galaxies. In an effort to maintain viral security, sections of the city were sealed off and sanitized before the Lantean project began. The Alterran physiology was retarded back to what is approximately present day Human level and the first of this new seed species was grown in maturation labs...thus the first Lanteans were born.
Despite the fears of unrealized contamination, the Lanteans never contracted the plague. As the remaining Alterrans in Atlantis either died out or ascended, more and more of the city was sanitized and turned over to the growing Lantean population. Before the last of the Alterrans died they left the Lanteans with one mission priority:
Use Atlantis and the technology within to rebuild their civilization...or at least preserve it for the coming of the more inferior seed species in the other galaxies.
The Lanteans were given other instructions, such as establishing a stargate network on a special frequency that wouldn't connect outside the Pegasus galaxy. The Alterra insisted on a strict quarantine...any travel outside of Pegasus might contract the plague. The Lanteans were to remain and develop isolated in Pegasus.
Due to seeing their progenitors ascend during those first few years in Atlantis, Lantean culture held achieving ascension as its primary objective. So much so, in fact, that they developed a pacifistic attitude that greatly hindered their later war against the Wraith.
10,000 years after the Lantean defeat and retreat, the 2nd generation of Lanteans was established. see Lanteans2