Magnus (AMANDA TAPPING) returns home from an overnight trip to find the Sanctuary in a state of confounding chaos: Battle debris everywhere, no one in sight, and a scheduled UN Security Team inspection just hours away.
The exodus from Hollow Earth begins, and time is of the essence as the Sanctuary stands between the abnormal refuges and the demanding UN. As they try to maintain peace, Helen receives a surprising warning from an unexpected source.
With Magnus gone, Will is appointed the head of the Sanctuary Network. The abnormal uprising continues to get worse. Biggie and Kate are kidnapped. As expected the surface governments respond to the uprising with deadly force.
The UN Security Council sends a task force headed by a weasel of a man, Greg Addison, to investigate the Sanctuary. His disdain for abnormals is matched by the disdain that Magnus and team have for him.
Since the UN no longer backs the Sanctuary, Magnus makes other arrangements for her finances. A planned meeting in Africa with a potential banker turns into a hostage situation. Will and Henry search for an abnormal in the Old City tunnels.
Will's trip to Liberia turns bad when he suffers a head trauma from an attack. The trauma brings up powerful memories about his mothers death and the inadequacies of his father. Magnus deals with be-winged scam artist.
FBI Agent Abby Corrigan's life is endangered after she is suddenly attacked by an unfamiliar abnormal during an investigation; Magnus and Will's heated debate over the best way to help Abby threatens to permanently alter their relationship.
There is a sentient organic nanite causing havoc in the computer system in the Sanctuary. Magnus and Tesla connect their minds to the system in an effort to isolate the nanite. They find Adam Worth instead.
A radical group of abnormal beings plan a terrorist attack with the goal of starting a war between surface dwellers and hollow Earth inhabitants. To Magnus' disbelief, Addison, at the NSA, has proof of Biggie's leadership of the group.
When the Sanctuary is approached by an abnormal leader about a radical plan for peace, Magnus goes all in and pledges her full support. However, when Will is forced to leave the Sanctuary, his decision may just put everyone at risk.
SCIU has surrounded the 5th Ward with troops and an electric shield that prevents them from leaving. Caleb has a virus that can turn the human population into abnormals. Magnus enacts her ultimate plan for the Sanctuary network.