In Triarchy once the Atlantis expedition is classified a threat to Earth and is to be terminated, the Atlanteans have no choice but to shut themselves off from Earth and adapt and change accordingly. Elizabeth and John solidfy control over Atlantis, turning it into their colony more than it ever has before. Teyla leaves to guide her people, as prophecy has long demanded. Caldwell maintains the Alpha Site and Lorne ferries the Daedalus between all three groups, continuing to negotiate between the three separating factions. Friendships change, strain, break, and grow.