What if you find a planet that pretends to be iron/medieval age but in reality it's a cover up to lure exactly the right kind of scum.
Bait and switch actually sounds kinda fun. A little contrived but it might be lulzy to run.
They come in believing a easy prey awaits but soon discover they fallen into a trap, the locals do have technology beyond crossbows and your ship has been boarded and being overrun to be resold while you are left stranded planetside (your transport is blown up or something and none are coming from the ship).
The crew compliment is 26k. That's without counting the actual House soldiers or elite troops in Power Armor with Melta Guns on board. Seizing an entire starship is actually not as straightforward as one would think. Which is why it would seem a little contrived to have a planet of pirates masquerading as savages. One would think it would be simpler to just wait at the warp translation point and jump the first ship that comes out of the Warp when it's blind and struggling.
Then the warpstorm hits.
While that is totally thematically appropriate for 40k, it kind of violates the primary rule of table top roleplaying (IMO) where players need to be able to do something in the face of X. Being caught in a warpstorm doesn't really leave the players a lot of options other than "don't die." While it's great for newbies or easy going roleplayers, veterans with a strong sense of fun vs. not fun and what's fair can sort of see through the narrative and can often resent situations designed purely to put them through ordeals with few options for them to act on.
That and I did write up my psychotic warp travel procedure so I could make "warp stuff" a regular part of gameplay. (So far, some of my most effective warp events have actually been 100% flavor things that became something more in the minds of the players. God I love Warp-based paranoia.)
Mutiny plot -> make the crew want something (or something) and once Captain goes to blow their brains out, make the whole crew flip their shit (bonus points for Chaos cultists) so in the end the team is captured. The ship arrives on destination or somewhere and then they must bust out of it and get help, but once they leave the ship the mutineers should notice what is going on and warp the fuck out. Then make the party have to go long distances to retrieve the ship, and if they try full frontal assault instead of doing something more subtle, they should be forced to destroy it because fuck those guys.
I get where you're coming from (man I'm just full of nay-saying right now) but a couple things:
-The players were inspired by like old-timey high seas adventure. "Master & Commander" is what they're going for. Their crew is populated by 'hard men' from the captain's own planet, and they joined him on his revenge quest against this Ork Freebooter that wrecked their world. So up until now it's all been very "Yes sir!" and "We won't let you down Captain!" and "you heard the Captain!" and "Death to Grom Kol! YYEEEARRRRGGGHHHH!" Having the entire crew mutiny on them both would reverse what the theme has been so far....and the players haven't really done anything to warrant it. Yet.
-Mutiny is already part of the rules based on how bad crew losses are and how much shit they've been put through, how long they've gone without shore leave. I'd prefer to let a real mutiny organically arise from that. That way I'm free of accusations of rail-roading them.
-I planted an unknown number of sleeper cells of saboteurs on the ship. Basically they're men from a disgraced house that considered itself the archenemy of the Captain's house. After their disgrace, they signed away their lives for a chance at revenge against House Kincaide, joining teh crew under false pretenses and succeeding since the Captain needed every warm body that would say yes. The players have already "foiled" a number of sabotage attempts. I'm just waiting for the right opportunity to do something else. So far it's been sabotaging munitions or planting bombs around the ship. I'm tempted to have them attack someone in their quarters next time. There are plenty of people already who bear the ship and crew ill will. I don't know if I need to turn their whole crew against them. It's also a lever I can use when, in the middle of something truly dire, the saboteurs can make the situation even worse. (As an aside, they caught one of the saboteurs and turned him into a servitor that picks up dog shit on the bridge. They named him Doodles. These are my players.)
Also I got an apology from a friend for basically being immature dicks at table. That went a long way toward soothing my ego.