Magnus meets with Caleb, Caleb tells her the Hollow Earth abnormals acted in self-defense, but that the conflict with the surface-dwelling humans is no sollution. Magnus asks Caleb what she can do, and learns that he wants to create a settlement for abnormals in Old City's Fifth Ward.
Magnus takes Captain Franklin, local head of the SCIS, to a hideout where they meet with a number of abnormals and discuss the possibility of a peaceful coexistence. Magnus, Typhuss and Caleb break a number of abnormal prisoners out of an SCIU detention facility. Addison orders Will to arrest Magnus and Typhuss.
Later Will and Captain Franklin ambush Magnus and Typhuss, but they get away. Will goes after them on his motorcycle while Franklin calls for backup. A chase ensues, but ends with Magnus and Typhuss running into a dead end. Will tells them they are under arrest. Magnus knocks out Will and gets away with Typhuss on her motorcycle just as Abby and the backup arrive. Back at the SCIS, Addison tells Will that he will handle the situation personally now.
Later, Magnus and Typhuss meet with Caleb, Magnus tells Caleb that they might have to redirect the overflow of abnormal refugees to other Sanctuaries, but he refuses to turn anyone away. Later that day Magnus and Typhuss are led to Caleb and Magnus tries to convince him that the Insurgency should go into hiding for the time being. Magnus also tells him about the containment field, but he decides that he and his kind should make their stand.
Magnus finds Caleb at the Sanctuary's front gate, and he is not alone: Caleb and his abnormal brothers have come to attack the Sanctuary. Magnus sarcastically welcomes them to her home, gun in hand. Magnus fires a number of shots at Caleb, which hardly slows him down. Magnus retreats inside and tells Henry to lure the intruders to the main lab. Henry and Typhuss both gear up and prepare for battle. Meanwhile Will and Abby arrive in the Homeland Project and start evacuating the abnormals.
Typhuss and Henry use their stunners to overcome two of the intruders, while the rest is after Magnus.
They catch up with Magnus in her main office, but she is able to slip away.
Will finds and frees Kate and minutes later they and the others are on their way out of the Fifth Ward. Magnus arrives in the main lab and sends Typhuss off with a kiss. Typhuss locks her in the lab just before Caleb and two of his brothers arrive. The automated guns take his companions out, but Caleb hits Magnus, sending her flying through the room. Magnus punches another button on her control pad; an automated arm with a giant drill punches through Caleb's upper body from behind, killing him. Five mintues later Typhuss and Henry enter the lab with their stunners ready but the battle is over.
A year after the battle the Sanctuary team abonanded the Sanctuary in order to go into hiding at the new Underground Sanctuary.