Doctor Who/NSS4 E10 Midnight/WMG

That thing was The First.
Considering the fact that there would be trillions of humans by then it's reasonable that the evil in the universe would also increase. The existence of Evil keeps the First in existence so it could stand to reason that more evil would make it more powerful.

The Doctor was still contaminated... and may still be.
OK, so the person who infected him is gone and he can talk again. Somehow, her being dead frees him, even thought he thing responsible for all this lived out where nothing can survive. We're talking about a guy who regularly repeats things. When his best friend, shortly after this, absorbs part of his mind, he suppresses all memory of him and all of his personality over her protests. We later find out that it isn't quite as dangerous as it seems if she remembers, though we never do see her get it all back. After her, he refuses to take any other companions and is constantly fearful, but also in some ways eager, for his "death." When he finally regenerated, he no longer seems concerned with any of this, eagerly seeking out a companion. Clearly he thinks he burned it out. But he's been wrong before.

The entity was a surviving creature of the Time War.
A nameless horror that gleefully prods people into becoming monsters sounds like it would fit right in with "The Nightmare Child" or "The Skaro Degredations." But the real evidence for this is that when the Doctor restores the Timelock in "The End of Time Part 2," the music playing comes from the Series 4 track for this episode. The Emperor's ship fell through, so maybe the Midnight creature did as well.
 * Specifically, it is (or was) a member of the Horde of Travesties. A "travesty" is a distorted representation of something, and the Midnight entity copies the behavior of others, thereby becoming a travesty of another being. If so, there are more.

The entity wasn't an entity, but a phenomenon.
The Doctor said himself -- they were the first to be in (and see optically) that specific region. The "shadow" was noticed by the mechanic, who (along with the pilot) was the first victim. The area enhances psychic fear, allowing it to manifest empathically and psychokinetically. The Doctor's uncertainty about the "shadow" caused the knocking; the increasing fear by the mechanic caused the cabin to get destroyed. The increasing fear about the knocking couldn't get "in" physically, but got in psychically. Skye's increasing panic made her the juiciest target; the Doctor's sudden jump in fear at being put under the microscope made him more vulnerable. Fear feeds on fear; fear experienced in that particular location of the planet amplifies it and gives it form, but it isn't sentient in any sense.

The entity was actually Skye the whole time, capable only of feeding on fear and causing fear-induced hallucinations.
A plausible chain of events follow thusly.


 * Skye's the first (only?) person to notice the Doctor is not what he seems (she spots him using the sonic screwdriver.) Once it realizes it's got interesting prey, it gives the pilot a hallucination to get them off course, making sure that a handful of ordinary people are going into an unusual location, one that was never explored before.


 * She seems to encourage the Doctor's cheekiness, and encourages the suspicion of him later; she's even the first to speak to him when he comes back from the cockpit, adding a stressful tone to her speech and reacting dismissively to the Doctor's assurances.


 * She causes the knocks, then says "Is there something out there?!", presupposing that there could be something outside the craft.


 * She also claimed the knocks "answered", planting the concept of communication with something unknown, and shut down the hostess when she tried to calm the group.

Viewing her behavior in this context, her panic is perfect; she's helping the rest of the group crack. Her breakdown of "it's coming for me, it's coming for me" gives the rest of the group a horrible thing to imagine happening to each of them in turn. She even turns on the entertainment system for a second or so when she shuts down power in the pod. Simple hallucinatory phenomenon meant to fuel the fear reactions of the passengers explains the knocks, and once a creature is scared enough, she can effectively preempt its higher thought and motor cortex; hence, no movement, hence, only speech. Once the Doctor was scared enough, his only chance was for one of the other passengers to save him.

If true, one might say the worst fear of the Doctor is that humans will abandon him, even turn on him.

Midnight is PSR J1719-1438 b.
Both are planets made of diamond, whose star emits deadly radiation and should render the planet totally uninhabitable.

There was no entity...
] At least, not the one we think it is.

The, for lack of a better phrase, "monster" was capable of really nothing, when you think about it. Disagree? Well, let's see what it did during the course of the episode: And, that's it really. It didn't do much else.
 * Copied speech
 * Stole other people's voices

Now, let's say something could have been out there. If something could survive the x-tonic rays, it doesn't necessarily mean it was the thing in the charter. Maybe the Midnight Entity had incredibly thick skin, or had somehow built up a tolerance to the rays. It would explain the thumps, the missing cockpit, and the responses to the knocks. However, this leaves one question that urgently needs to be answered:

The fuck was that thing?!

We never learned what species Skye was, now did we? Maybe she was, as an above WMG suggests, some kind of alien species who fed off fear. And the fear of the Midnight Entity caused a feedback, of sorts. So, she shorted out, so to speak. Then, she rebooted, mimicking other humans voices. The feedback of Skye's blackout interfered with whatever makes a time lord tick.

She Came Back Wrong.

It Got Worse.

The entity was a virus.
Viruses can play dead until they find themselves a new host, then they resurrect and wreak havoc on the new host's body. This would enable the entity to survive in an environment that was previously assumed to be uninhabitable, because it would mean that technically it WAS uninhabited: the virus WAS dead, until that nice bus full of new hosts arrived to bring it back to life.

In addition, viruses can affect the brain as well as the body, which would make it somewhat scarier because hysteria and hallucination could be symptoms of the virus.

The only things I can think of against this WMG would be how the driver and the mechanic were killed in a way that involved the bus being ripped in half, and why the virus would affect humans and time lords similarly.