No, the Doctor's definitely nowhere in sight. And, as usual, it was his own big mouth that's the cause of it.

He tipped his hand a little too much in the elevator; gave away too much information. As soon as that prat found out that the Doctor wasn't human, the security man had popped him in the back of the neck.

He comes to shirtless and bound by the wrists in some kind of examination room. And that's where the truth comes out. He's not a collector. He's a scavenger. He loots and pillages, reverse engineers them, and then patents them and makes a killing. Which is why no matter what he says to van Statten about the Dalek, he won't listen. He just keeps scanning him with that really sodding painful machine.

And now it's just a matter of time before everything goes wrong. Again.