When SCIU turned Caleb's surface-dwelling Homeland into a prison, Magnus knew their intent was to kill, and when Henry finds energy nodes - an invisible fence invented by Tesla but perverted by SCIU to be deadly, that clears up any doubts. Henry and Tesla attempt to remotely disarm them while Magnus buys time by announcing to the media that monsters are real.
But SCIU isn't the only enemy to watch out for: Caleb, the onetime leader of the Hollow Earth insurgence, has designs to weaponize a mutagen that will bring forward the latent genes in humans and turn them into Abnormals, a move that will make every human on Earth dependent on this twisted revolutionary and his followers.
And Addison, finally seeing the nefarious side of his superiors, turns to Will for help in anticipating Magnus's next move - but Will, by Addison's orders and Magnus's secrecy, is hamstrung. Addison restores some of Will's clearance, and he and Abby set about on a detective spree that leads to the bottom of Helen's centuries-old plan. They discover that, under an assumed name, Magnus worked with some of the finest minds of the twentieth century, built a secret network larger than Will thought possible, and closed down Wall Street so she could liquefy all her assets without anyone knowing.
Biggie, who has moved into the Homeland encampment, shows his true fidelity when he steals Caleb's mutagen and delivers it to Magnus, and this costs him the ultimate price. Caleb and his cronies deliver Biggie's martyred body to Magnus's door, demanding her blood, as well. But they didn't count on the secret weapons she has stashed in the Sanctuary, namely, the vampiric wrath of Tesla and Henry's pure HAP pain. The henchmen gone, Helen lures Caleb deeper into the bowels of the Sanctuary, but precisely when Caleb thinks he has Magnus on the ropes is when she launches her final weapon.
In a tit for tat, Addison sets up enough smoke and mirrors to ration enough time for Will to clear the Abnormals out of the concentration camp. But when he arrives at the Sanctuary with truckloads of refugees, he gets the same surprise as Caleb: An incinerated Sanctuary. Nothing left, all ash and flame. Will is annihilated: Biggie was murdered, his life's work is destroyed, and Helen Magnus and the Sanctuary are gone.
Or are they? Not much later, Will's mercurial employer appears as if from the dead, finds him and takes him to a remote place. Her scheme, all this time, was to build a new, better Sanctuary. To Will's wonder, Magnus reveals a Sanctuary large enough to hold the world's Abnormals - and it's all underground...