When Helen Magnus and the Sanctuary team first ventured into Hollow Earth their tracking beacon disappeared shortly after they passed through the gateway. John Druitt wanted to telaport to Hollow Earth to rescue them, but in order to do that he needed exact coordinates so in order to get them Nikola Tesla hooked the brain sucking spider robot Adam Worth sent after Will to the Sanctuary main frame. However, before disconnecting the spider robot it left a nanite in the Sanctuary computer system that could've taken over the whole system if Tesla hadn't quarantined it in a hidden section of the software behind a "fort knox" of firewalls.
The nanite escaped when Magnus asked Henry to move their more sensative files to a more secure network, durring the transition the Sanctuary's firewalls were down for a nanosecond which is when the nanite escaped.
The only way they could quarantine the nanite again was for Magnus and Tesla to download their minds into the Sanctuary computer and quarantine the nanite in cyber space.
Once inside cyber space, Magnus and Tesla found themselves in a virtual Sanctuary inhabited by Adam Worth (A.I.). At first the A.I. was helpful, but then it tryed to trap Magnus and Tesla in cyber space forever and take over their bodies. Howeve, Magnus out smarted the A.I. and was able to quarantine the nanite.