Well, Jamie got himself and the Doctor captured again while looking for Zoe and Isobel. I am sure that won’t cause problems.
Yes, captured by Vaughn, but he really wants the Doctor to explain what the weird circuits are and what they do. The Doctor might help, and Vaughn has the perfect way to get what he wants, namely the promise to take Jamie and the Doctor to Zoe and Isobel before the train the two women were put on departs.
Yes, Vaughn tells his head of security to make sure the train leaves before the Doctor and Jamie can get there, ensuring the two men will go with Vaughn to IE’s main post, where he has a private army and the mysterious Professor Watkins that the Doctor was originally looking for.
Wait, wasn’t UNIT keeping surveillance on the building? Yes! Can’t the Brigadier rescue them? Eventually! He can’t move unless the Doctor gives a signal because, you know, private army and all that. So, he can have the car followed by a helicopter until they get to the base, and that’s that.
By the by, Vaughn tries to impress the Doctor by showing off he has an office here identical to the one he has in London. I don’t think that’s so much impressive as having a good excuse to not spend money building another set. Still keeping the two from the women, Vaughn has the Doctor and Jamie sent down to see Watkins with the intention of watching the conversation over a video camera. The Doctor, however, knows he’s being watched and uses a gadget to block the TV transmission before Jamie can say too much to Watkins, who thanks to Professor Travers knows all about the TARDIS. That sends Vaughn down to have the Doctor and Jamie grabbed with the idea being he can maybe torture answers out of them. As such, he hands the two off to his head of security.
But this is the Doctor we’re taking about. The security guy is, of course, stupid. He falls for a simple trick where the Doctor offers to tell what he knows while Jamie preps and elevator, but then shoves the dumb guy out of the way while he and Jamie escape by going up and then sabotaging the elevator so it breaks down between floors.
But Vaughn says to override the thing and check it!
But the Doctor and Jamie escape through the roof hatch and begin climbing to the roof!
But the security guy figures that out and has the elevator overridden so he can follow them up to the roof or kill them!
But the Doctor and Jamie get to the roof first and find a fire escape!
But the security guy…did not send men out to guard the fire escape.
See, that guy is dumb.
As it is, the Doctor and Jamie do find a train car that has more of those pods in them. Men come to search the car. The Doctor hides in one place while Jamie jumps inside a pod to hide.
And something in there is moving…