All in all, it took a combination of the ex-Arbite leaping onto Wilhelm's back and pounding his skull with a shock maul, two of their biggest Enforcers (equipped with massive two-handed Cyclopea-Pattern shock mauls, capable of flipping cars) taking out his knees, and the timely arrival of Jayne with a needle rifle loaded with sedatives to put the Space Marine down. (The toxin is normally active within seconds of a single dose - she shot him in the arse four times, and it still took about 5 minutes to take effect, with the Enforcers still wailing on him to keep him down long enough).
They dragged the unconscious Astartes to a nearby holding cell, and when he woke up shortly after, the Lord-Captain had the joys of interrogating him. As a precaution, she had the Ecclisiarchy on board the ship check Wilhelm for the taint of the Ruinous Powers, and had Jayne waiting outside with the biggest weapons she could lay her hands on. Wilhelm explained his findings regarding his Chapter to the captain, and apologised for letting their betrayal affect him so. He had fought valiantly alongside his Brothers, in The Emperor's name, for centuries before the Inquisition pinched him - he even claimed to have fought alongside the Traitor Primarch Angron before his Fall.
He claimed that the Inquisitor who took him was working for the Ordo Chronos - a group dedicated to eradicating paradoxes caused by the Warp's fluid sense of time and continuity. He had just so happened to appear a few years before the Heresy, and took advantage of the fact to lay his hands on what were once the Imperium's most feared Astartes.
Claudia offered him a choice - either clean his act up and start working off his debt (he had murdered several dozen workers in his rage and caused a lot of property damage), or go throw himself to the mercy of another Chapter, who would most likely have him killed. Or crawl back to the Inquisition, where his fate would most likely be far worse.
Claudia left at that, in a rage at his behaviour. About an hour later, she received a vox from the Aleph-Five Enforcers - he was back in the area, without his armour, going door-to-door and apologising. Aleph-Five held around a thousand people, so he might be at it for some time. She ordered them to keep an eye on him, and sent Jayne to tail him. He spent several hours trailing through the district, offering his condolences to the families of the deceased and assisting with the clean-up.
By this point, the ancient ship, now christened The Champagne Room, much to the chagrin of the ship's AdMech contingent, had been restored to be at least able to move, and could follow the Vegas through the Warp (though it seemed to not require a Navigator to do so). As such, the crew resumed their journey to locate the third and (hopefully) final chunk of the Eldar starmap. Allesaunder had pin-pointed the most likely area - a small, recently settled moon of a large planet, a fortnight's Warp travel from their current location. The journey was uneventful, barring a few moments of lost gravity and strange dreams for all the crew.
Except the Lord-Captain - following her recent encounters with Eldar technology, and finding new pieces to the ancient starmap, her "visions" of the Pearl through the eyes of another were becoming disturbingly clear. She felt a deeper sense of memory, and even began to catch sights of her "other" self in reflections, just at the corner of her eye... these developments worried her. Enough that she had the Medicae and Chymists work her up some incredibly powerful stimulants, enough to keep her awake and functioning for up to 5 days at a time (with only minor side-effects), and powerful sedatives for when she did sleep, to stop her from dreaming. While this meant she had far more time to catch up with paperwork, she worried at the effects it might have on her sanity.
The crew began a full sweep of The Champagne Room, to see what secrets it may hold. Along with the fruit and veg (of which they found a surprising amount), they located a few hangers full of "space clothes" (the Captain is not a creative namer), made of an unusual fabric, capable of keeping you at perfect room temperature regardless of current temperature (extremes notwithstanding), which vaguely resembled tinfoil jumpsuits, a couple of ancient weapons in varying states of disrepair, a surprising number of "modern" weapons, and some odd bits and pieces. These were transferred to the Vegas, in preparation to be sold off.
After a good few weeks and a few course corrections, they had arrived at the uninhabited planet Allesaunder had deemed most likely to hold the final starmap piece - and were surprised to find an Imperial World. The planet had only recently (as in, in the last 50 years) been settled, and were still waiting for the Administorium to contact them to confirm that they even existed. As far as they could see, it was a true Frontier World - a lot of deserts, and the main population centres were focused around huge cathedrals (which they later learned had been air-dropped onto sites most hospitable to life).
The Lord-Captain, crafty bugger she is, decided to get on the inhabitants good sides first, and played the proper Rogue Trader - presenting the locals with a great show of wealth and status, laying on a drinks reception and a show of wares (mainly silks and foodstuffs). She was welcomed by the locals with great fanfare, and they offered her minerals and materials in exchange. As they were of a tech-level resembling the Old West of Terra, their offerings were not much - but she accepted them graciously. Finally, after much charming and chatting, she was allowed to arrange an expedition out into the uncharted deserts - where local superstition had deemed that "ghosts" dwelled.
"Great, terrible ghosts... skeletons, fingers like butcher knives, faces like cold, metal skulls..."
They Away Team (including Wilhelm, his armour now redecorated to remove any reference to his previous Chapter, and bearing the colours (if not the insignia) of House Black) decided to head of the next morning, catching some well-needed sleep before the gruelling desert travel that awaited them.
When they awoke, it was to screaming.