After the first two eps of season 2, I have lots of fun guesses about what may be going on. I'm gonna toss 'em out for discussion...

Tom isn't mind-controlled because the Overlords don't have a practical means of mind-control. If they did, they wouldn't need harnesses. Ergo, if Tom is not harnessed, he is not being mind controlled. He can stop worrying about that. The Overlords have amazing biotechnology, but it's not magic, and their power is not unlimited.

However, the thing in Tom's eye shows that the Overlords do have the capability to implant all sorts of super-nasty tracking/spy devices in human bodies. Tom's dream in the tent where the red-eye/scarface skitter grabs him by the neck and leans in close was a memory of what happened while he was held captive. Scarface was transferring that metal bug thing from his eye to Tom's eye. Scarface may be the Overlords' "spy master", in which case he's used this trick before...

Furthermore, the fact that only Tom was very intentionally not killed when he and all those people got off the ship in Michigan shows that someone - either Scarface or the Overlords - wants him alive. Why? So they can track him! And by extension track the 2nd Mass.

(It's even possible the Overlords are intentionally herding the 2nd Mass towards the remnants of the US government, to get Tom in with the remains of the US government, to track them too. The little girl with the motorcycle? Could have been harnessed. Her hair, scarf and parka covered a lot...)

Pope's analysis of the situation wrt/Tom is dead on, as his analyses almost always are. Pope's failing is that he never picks the right solution. But he's usually dead on about the problem.

Other things...

Everything the Overlords ever say to directly to anyone is deceptive, either outright or by omission. We can assume that everything the Overlord said to Tom via Karen was either a lie or attempt at manipulation. That was also far from the first time the Overlord has given that speech. Tom's two sentences with the military woman from the Maine Irregulars(?) show that the Overlords have been giving that speech to tons of prisoners, in an attempt to convince them to lead humanity into prison camps/reservations. (The allusion to the Trail Of Tears was particularly good. Nice job on the writers' part.)

The Overlords are like the Roman Empire, conquering and colonizing various foreign nations. Earth is just another colony to them - something to conquer and extract resources from. And that process is easier if you have some quislings among the native population. This also implies that the Skitter planet was probably one of the Overlords' previous conquests. (Makes you wonder what the Skitters looked like before they were harnessed. Probably the same number of arms and legs, but drastically different color and texture.)

The brain in the aircraft wreckage that Ben found might be a Skitter brain. The Overlords more than likely have the biotech to do that kind of thing, and have plenty of experience modifying the Skitters.

In spite of all their technology and military power, the Overlords do seem a bit frustrated. Karen's bit about "there's no reason to prolong hostilities" shows that they're surprised at how difficult mopping up the last of humanity has been. The obvious emotion behind "don't overestimate these small victories" shows the same. Humanity is proving scrappier than they expected. But the eventual outcome... is still very much in doubt in my mind.

Okay, enough rambling. What do you think about my guesses here?