Magnus awakes to find that the mind spider - the organic Praxian device that absorbs people's thoughts - has escaped from its containment unit. Based on the fact that the lock on the spider's cell was unmolested, Henry realizes that the mind spider is responsible for the multiple security glitches the Sanctuary has been having recently, and may have created a secret data branch, heavily protected by firewall after firewall. As Henry discovers this digital cache, Tesla arrives and demands to know how they found it.
In a volley of blame, the team discover that a sentient, organic nanite is loose in the security system and could take down not only the Sanctuary, but the whole world's computers unless they stop it, and the only way to do this is to transfer their minds into the digital world - a potentially fatal operation.
In this virtual reality - a near-perfect representation of the physical Sanctuary - Tesla and Helen are greeted by an interface that resembles Adam Worth but lacks his knowledge of their shared history. They enlist his help in finding and quarantining the nanite, which he affects to do, but they soon discover he has learned of their historic animosity and trapped them in his playground in revenge.
Helen and Tesla manage to distract the digital Worth long enough to send a message to Henry, asking him to send Will in after them, but when Will arrives, Worth demands that Helen make a choice: Adam will transfer his virtual consciousness to someone's body, either Will's or Tesla's. Who will it be?
Helen chooses Will, and Adam begins the transfer. But when he attempts to resurface in the physical world, he discovers that he has been duped - Henry built an image of Will, created patchwork-like from Helen's memories. Since he's not really Will's consciousness, Worth has essentially done away with his own virtual identity in exchange for a shadow self. While this maneuver was underway, Henry was able to put the nanite on lockdown and fully disable Worth.
The nanite is no longer a threat, and Worth's consciousness is forever trapped in an isolated drive. What information they were able to glean about Praxis is likewise stored and sent with Biggie to help with the efforts at rebuilding that venerable society. The world that Worth once helped to destroy may now be rebuilt by his very own memories.