See, I knew the Doctor would prevail as soon as the Chameleon Director started saying how he and his kind were the most clever race in the universe.
It turns out the Doctor had them beat even before he stepped foot on their satellite.
The Doctor even tries to be merciful. Just let everybody go, and the Chameleons can go back where they came from, and he will never hold anything against them in the future. He’s not even mad they made a Jamie copy. He’s mostly disappointed the copy didn’t get the Scottish accent.
Of course, by then Samantha and the Commandant’s assistant found the missing humans. Mess with the armbands, and the Chameleons disintegrate. They even do so to one, and that is enough to cause a revolt against the Director by the ones with copies still on Earth. The Doctor said that would happen. Sure, he was bluffing for time, but he did say as much. He’s sympathetic to the Chameleons. He just knows abducting 50,000 young humans to fix a problem on their homeworld is wrong.
And given how many times I have seen any Doctor promise to forgive and forget against any number of alien threats, it’s nice for one to actually take him up on the offer. Sure, the Director and the Jamie clone don’t, but they get killed by their own kind as a result. I’ve seen plenty of aliens and even some humans refuse to walk away, and the consequences for that are always bad because the Doctor means it when he says he’ll forgive and forget. Most of these beings just don’t seem to get that, and you really don’t want to anger a Time Lord if you can help it.
So, the day is saved again. The Doctor finds Jamie and Inspector Crossland, then returns to Earth with Jamie, Ben, and Polly. Once there, Ben and Polly realize that the date is basically the same day they accidentally boarded the TARDIS, and they opt to stay behind. Not a bad goodbye. Granted, the two of them sat out most of the serial, but as goodbyes go, it seems to have basically worked out in their favor. Were they particularly memorable companions? Not really, but they weren’t obnoxious or anything. They were just standard sidekicks for that era. Arguably, the companion with a distinctive personality beyond “stock heroic and helpful” may be Jamie, and he’s sticking around for a while.
Heck, Jamie got a nice kiss from Samantha. Too bad she couldn’t become a new companion, but this is the last serial before Victoria joined the TARDIS crew.
Which may be why the last few lines has the Doctor revealing to Jamie that, yes, they got the TARDIS back from airport security, but someone just stole it.