In ‘The Lodger’ the Doctor discovers a mysterious time machine, using a perception filter to disguise itself as the top floor of a flat. While we don’t learn who owned the time machine in this episode it is suggested in ‘The Day of The Moon’ that it belonged to the Silence.
By the time of ‘The Time Of The Doctor’ we know that the Silence were time travelling into the Doctor’s past. The real question is whether the time machine in ‘The Lodger’ is the same one the Doctor encountered in 1960s America or if it is just the same model.
The Doctor seems to think that it is the same machine, as he believes he is about to find out how it came to be abandoned. At the end of ‘The Day of The Moon’ the Silence have unwittingly caused humanity to rise up against them.
This combined with River Song shooting them could have resulted in the death of the Silence crew. It could be that after they died the AI managed to fly the ship to the UK (probably not long before the events of ‘The Lodger’) or that one of the Silence lived long enough to put the ship in motion but died causing it to crash.
We do know that the ship in ‘The Lodger’ did crash, the AI states as much. It states that the crew is dead and it is seeking a new pilot. The fact that it crashed strongly suggests that it didn’t mean to be in this time and place. If it isn’t the same time machine form ‘The Day of The Moon’ where was it heading?
You may wish to develop the backstory of the time machine, possibly having the PCs be responsible for its crash. Did the crew die or did they manage to escape? It could be that the PCs were protecting the Doctor from another attempt to meddle in his past.
The control orbs and resulting electricity effect of the time machine fit with members of the Silence being the crew. The ship was looking for people who wanted to escape to enable it to leave (to where?). This could suggest that other examples of Silence technology use telepathy.
The Doctor’s statement that someone was ‘trying’ to build a TARDIS suggests an amateurish attempt of imitation. While it is possible that the Silence were trying to copy the greatest weapon of the Doctor, his time machine, it doesn’t match what we see of their technology.
The Church apparently have extremely efficient time machines, able to go when and where they like. Was this time machine a prototype? The crash and death of the crew would certainly suggest that this is its first flight.
It is also suggested that the Time Engine will destroy the planet if it takes off with a new pilot and could destroy the solar system if the Doctor is the chosen pilot. This would work against the human-founded church so this is either a flaw they were unaware of or the Silence have rebelled and don’t care about the fate of humanity (possibly still upset about the events of ‘The Day of The Moon’).
The ability of the Time Engine to use a perception filter could make the Silence and the Kovarian chapter much more dangerous. This allows them to conduct covert operations, using time machines that don’t just camouflage themselves but convince people that they were always there.
The AI is able to come up with a plan to replace the pilot, using its holographic display to lure people upstairs. While single-minded in pursuit of its goal, the Doctor suggests it would work its way through over 6 billion people which seems a bit far-fetched, this does show some imagination.
We haven’t seen any other evidence of the Kovarian chapter or the Silence using such advanced AI, although it does make sense since they were an off shoot of the Papal mainframe.
It would also make sense for the Silence to make use of machine intelligence which won’t forget them. It could be that they used artificial intelligence constructs after they dissolved their links with the human members of the Kovarian chapter.
If the Time Engine had been able to leave with a pilot where would it have gone? It may have returned to the Kovarian chapter. If it had caused the devastation the Doctor predicted they’d need to find a way to repair the damage. Would they have been forced to alter the Doctor’s timeline so the events of ‘The Lodger’ occurred or would they turn to the PCs?
If the Doctor failed to stop the Time Engine would Amy have been sent hurtling into the vortex in the TARDIS? This could lead her to bumping into the PCs (possibly inflight) and needing their help to set things right. It is also possible the out of control TARDIS crashes and explodes on her wedding day, creating the original reason for the cracks in time.
Did the Silence of the Kovarian chapter investigate what happened to the Time Engine? This could lead to another adventure with Craig and explain why he moved between ‘The Lodger’ and ‘Closing Time’.
If the Kovarian Chapter are still out there (unaware of the conclusion of ‘The Time Of The Doctor’) they could continue to perfect the Time Engine. Might they actually be able to perfect their own form of TARDIS? Could this put them in the position to fill the place of the Time Lords?
PCs could encounter other Time Engines, hiding in the most unexpected places. If the ship’s original crew did die then others might have found it. This could place it in the hands of UNIT, Torchwood or less reputable collectors.
This could also be a way to put a time machine in the hands of a group of PCs without a Time Lord. They could find that the flat above them is actually a time machine (or the mysterious cupboard in their place of work or even a garden shed). As long as it doesn’t destroy the planet when they take off they should be able to operate it using the telepathic interface and the ship’s AI.
If things go terribly wrong it could be that their Time Engine is the one encountered by the Doctor in ‘The Lodger’.