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.

Following an assassination attempt on Senator Padmé Amidala, Jedi Knights Anakin Skywalker and Obi-Wan Kenobi investigate a mysterious plot into the heart of the Separatist movement and the beginning of the Clone Wars.