With the Ancients' city of Atlantis discovered in the Pegasus Galaxy by Stargate Command, Dr. Elizabeth Weir and Major Sheppard lead a scientific expedition to the ancient abandoned city. Once there, the team not only find themselves unable to contact Earth, but their explorations unexpectedly reawaken the Ancients' deadly enemies, The Wraith, who hunger for this new prey. Now with the help of newfound local allies like Teyla Emmagan, the Atlantis Team sets about to uncover their new home's secrets even as their war of survival against the Wraith begins.

One day, a city suddenly disappears. Takuya, a professional by-the-contract courier and lone wolf, meets Yuki, the only survivor from the city's extinction. The two rely on a message from Yuki's father, who was heard to be missing, and head toward the disappeared city, Lost. However, unexpected obstacles strike before the pair, with the reality especially shocking for Yuki. Before them are the feelings of those left behind, a mysterious group manipulating in the shadows, and unveiling the hidden conspiracy. Takuya and Yuki, who both were initially strangers, would deepen their bond during the journey and unravel the mystery of the Lost city.