You'll have to excuse the delay. We've been otherwise occupied with internal matters of utmost importance as of late.
The only vessels we're aware of the Runners operating thus far are craft provided by The Order or civilian vessels obtained on the standard market. If I'm not mistaken, there was mention of a Mobile Colony Ship at one point a very long time ago, but most of that data is irrelevant. Thus far, they're being monitored and I have no doubt that they may be providing information to your former employers, which may explain the sudden rise in Order activity around Liberty.
As for that warning - like I said, it's more than likely a fabrication to get away with dangerous or criminal activity within Liberty. Lying isn't above The Order or even their proxy organizations, so you can't be too careful. Mentioning a name that held a modicum of power gets people's attention easily.
Lastly, the class of Nomad was a Purifier, which - while rare - aren't overly uncommon. Still, something that large around Magellan is probably remnants of the incursion we dealt with. Stragglers that drift in and out of the houses. Unfortunately for them, we're equipped for tracking and revealing cloak-capable craft or husks alike. Any remnants will be found and removed, as will any signs of The Order.
- Leviathan
TRANSMISSION TERMINATED
Currently unable to consistently be present in the Community due to life constraints.