The Thonaris shipyards are a manufacturing and refueling shipyard facility in the Thonaris System, used by Omnius during the time of the Synchronized Worlds. Abandoned after the Butlerian Jihad, the facility remained idle until agents of Consolidated Transport discovered them, supposedly by accident.
Mentats Draigo Roget and Gilbertus Albertus had both surmised the existence of an the inactive manufacturing and refueling shipyard facility after studying shipping records from the days of the Synchronized Worlds. (Gilbertus later mentioned this to the Erasmus gelsphere, who confirmed that the Thonaris System did in fact host a large-scale operation.)
Acting on Draigo's mentat projection, Josef Venport acted on the information and sent an armed fleet of VenPort space craft to take control of the facility. There was rumor that Celestial Transport had already discovered the facility and had begun to utilize it to expand its space fleet. Upon arrival, Venport discovered that CT was using the facility, and its owner, Arjen Gates, was overseeing the operations. Venport quickly attacked and subdued the CT presence, with the added bonus of capturing (and subsequently killing) Arjen Gates, furthering the consolidation of space commerce for VenHold.
Using the knowledge of the existence of the shipyards as a bargaining chip to protect the Mentat school from Manford Torondo, Gilbertus shared his "projection" of the existence of the former machine facility to Manfred, who seized upon the opportunity to destroy the remnant of the Synchronized Worlds. Manfred led a Butlerian fleet of 200 Jihad-era warships "donated by" Emperor Julius Corrino to destroy every trace of the facility. Upon arrival, they were surprised to discover that Venport had taken control, and was utilizing the facility to full capacity.
A battle ensued wherein Draigo and Gilbertus were pitted against each other in a live space battle. Josef Venport attempted to negotiate with Manfred Torondo directly to preserve his facilities and keep Venport employees unharmed, but the negotiations failed and Torondo launched a salvo of missiles at the ground-based facilities, causing considerable damage and casualties. Outnumbered and desperate to hurt as many Butlerians as possible, Draigo negotiated a pause in fighting to evacuate VenHold personnel. It was, in fact, a ruse to launch functional (but otherwise abandoned) space craft directly into the Butlerian fleet and detonating them, causing chaos and destruction. When Gilbertus saw the ruse for what it was, he immediately advised the Butlerian fleet to assault the remnants of the Venport fleet. In an attempt to escape, Driago Roget and Josef Venport evacuated the facilities in an evac-ship, hoping to slip through the wreckage unnoticed. They were saved from destruction when Norma Cenva suddenly came to their rescue, folding a VenPort heighliner around their craft and then folding space again, transporting them to safety.