It's pretty obvious that this section of Lure of the Expanse tried to be pretty railroady and didn't even consider that players would be desperate to salvage the ancient Battleship. As such, many many many people on these boards have salvaged the vessel, or done something enough off script to skip the entire third part of the section, and I'd like to hear the stories!
My group recently "finished" this part of the adventure and made sure there was no way I could misunderstand that they wanted to salvage the vessel. Surprisingly (and thanks, I think, to the hell I put them through to get a GC refurbished) they had no intentions of keeping it for themselves, rather from the first moment they saw it they had decided to give it back to the Navy. I played up Captain Roth's madness as much as possible as they proceeded through the first couple parts of the adventure, wining over the Iron Kin, the Voidwalkers and the Wargars fairly quickly (our RT has a very high Charm roll and Unnatural Strength from the dinner on Footfall). During this period the hot topic of discussion was how to "care" for Captain Roth, with the RT deciding to just simply kill him when the time came. He prepaired for this by spreading a story to the tribes that the Oracle must die for the world to be saved, and he had himself presented as the Herald of change. They bought it hook line and sinker (due to good preperation on the RTs part, good rolls and the circumstance that he had 1k fanatical Drusian follows along for the ride).
After restoring power, the RT went to the bridge alone to talk to Roth. They already knew about the cogitator and where it was, so he was bassicaly trying to reason with the man. I went into drama mode, listening to the arguements, twisting them in the mad mind of the captain and then coming back with reasonable reasons why he should take the ship out past the edge. I had Roth seem less insane bit by bit during the conversation, before finally appealing to the RTs long term goals (the continuation of Drusus' campaign into the expanse). My player had a sad look on his face as he reached out and crushed Roth's skull, with an unhappy and sorrowful comment about the sad choice he had to make. So I had him roll 1d10 insanity, which pushed him over into a trama, and he rolled horrible for willpower, so he was struck mute for 3 days as a sort of repentance for what he did.
They won over the Pale Sons after speaking with the Mother and that was that. I gave them everything in the special hold (which honestly, won't unbalance the game to much further) and they'll get some ImpGuard equipment as per the rumor cutout. But they're also going to have problems getting all the systems to work right, and of course anything else I can think of as they try and get it back to the Calaxis Sector. It's going to cost them time though.
They've also ended up with a good number (10k) new Crack primitive light infantry in the form of the Wargar tribes, who have sworn fealty to the RT due to his amazing martial prowess. That's going to be fun to add to the Regiment of House troops that they've already got, along with the Drusians.
Luckily, I knew they'd figure out how to salvage it, so I've already worked out the reward from the Navy and the Imperium and how it'll tie into other storylines I've been planning around them. My RT said he actually felt bad about having to kill the Old Hero, and accepted the Insanity without question. The rest of the group were smiling the whole time we were playing that section out, and some even appeared to be about ready to cry. All in all it was a good session.