what appears to be a space ship, bring it on board and it has unknown sigils in it, a missing stasis compartment and a murderous ghost.
Our heroes arrive after the crew has lost one crew member to the killing ghost - and that crew member is now a ghost as well - and the crew has figured out that the ghosts have limitations - the ghosts cannot get into certain electromagnetically charged rooms (Faraday?) and disappear under the artificial "day" lights when all their systems go through multiple checks thus generating electromagnetic fields. The crew hides during the artificial "night" in their safe room and come out at 'day'.
Makes you wonder why the crew didn't just have the computer loop the artificial light day cycle constantly and therefore they could work and sleep in their own beds without worrying about night ghosts at all because there is no night.
Just as well it later proves that the ghosts can manipulate all the systems, but they can only use tools to kill, they can't kill barehanded.
The doctor isn't enthused about originally about the mystery, more worried about his Tardis - why she is scared and why she brought them here. Clara is still traumatized from the last episode, so she is superficially, overly so, excited about a new mystery.
The crew has lost their leader, so the 2nd in command takes over and she is a mute woman. OK, nice to include such people, but hardly efficient or safe, is it? Some of the crew apparently don't understand her and neither do our heroes, so she needs a constant translator.
They lose another crew man, the always unpopular corporate guy who had endangered their safety by ordering them to stay put instead of evacuating and destroying the facility, but turns out he actually saved the world by not releasing the ghosts on an unsuspecting topside, but he doesn't get credit for that. He gets killed and the doctor forms a plan to capture the ghosts. They do and realize with lip-reading mute woman that the ghosts are mouthing silently the same phrase over and over again.
The doctor realizes it's a message about coordinates. They use them to find the missing stasis compartment but don't open it. Because the last phrase may tell them who and why this ship was there. The secret lies inside the flooded town, inside a church...