The main story arc centers on Capricia and the other Atlanteans efforts to revive the remaining Atlanteans still in stasis and to find out what happened to the human race, and perhaps to a latter extent how to go through 'transition' themselves. The group goes through a series of battles with Negation forces who eventually attempt a full-scale invasion of Earth.
During this time the group comes across Australia hidden from the outside world due to a gigantic tachyon supercollider and find a 'transition' portal with humans getting ready to go through. They are attacked by a Negation squad leaving Tug blind for a time. Tug and Verityn then come across a 100,000 year old Atlantean named Aristophanes, a legend they had heard stories about as children. The group also feels the loss of Gammid to the Negation Universe via 'transition' portal which was meant to lead him and the remaining humans found in Australia to a "higher plane of existence" but instead takes them to the Negation Universe.
They meet a couple of 'cowboys' who aren't who they appear to be during one of Danik's tests and Terra Cognito feature considerably giving information on Earth and the state of the local galaxy. The twins relationship is explored throughout, detailing their rivalry and their relationship with Zephyre. Capricia and Danik come to an eventual understanding and by the end of the series the motives of Danik are evident throughout all of the Sigilverse titles.
The group eventually revive the remaining Atlanteans just in time to mount an offensive against closing Negation forces.