The Doctor kicks the button away from the Master with some Venusian Karate, then they are both captured by aliens. Locked together in the set that the Doctor and Jo were imprisoned in earlier, they immediately team up to investigate the alien writings on the walls. This makes it four stories out of four for Doctor-Master team ups.
Caldwell and Morgan have rescued Jo and taken her back to the dome, where Dent orders Jo to be put on the spaceship with the colonists. Caldwell and Morgan have an argument which brings Caldwell's character development arc - on pause (not paws) since the arrival of the Master into the story - back to the foreground. He disobey's Dent's order and takes Jo to follow the Doctor and the Master to the alien city.
The Master finally reveals to the Doctor what we have known since the start of episode one - that he knew about the doomsday weapon from the Time Lords' files. When the aliens come to take them away, the Master uses gas to allow himself and the Doctor to escape.
All the colonists are on their spaceship ready to take off, except for Winton who has a punch-up with an IMC guard. This fight lasts for a surprisingly long time considering it is between two minor characters.
The spaceship lifts off, and then explodes. It's another model shot, of course, but quite an effective one, assisted by way of a quick cut to Jo and Caldwell where we see their reactions. They think all the mannys on board have been killed, and Caldwell feels guilty because he helped the IMC baddys send them off.
The Doctor and the Master reach the doomsday weapon's control room. The Master says that with the weapon he could make the Earth's sun explode "now." The Doctor says
"That's unbelievable!"
"You know the Crab Nebula?"
"The cloud of cosmic matter that was once a sun? Of course."
The Doctor delivers this line as though insulted by the ease of the Master's question.
"That was the result of the super-race testing this weapon!"
Jo and Caldwell reach the alien city. An alien tries to capture Jo but Caldwell knocks it out so, for a change, they are able to get inside without having been captured.
The Master tempts the Doctor in what is surely the key scene of the whole story:
"Doctor, why don't you come in with me? We're both Time Lords. We're both renegades. We could be masters of the galaxy! Think of it, Doctor - absolute power! Power for good. Why, you could reign benevolently. You could end wars... suffering... disease. We could save the universe."
"No, absolute power is evil."
"Consider carefully, Doctor. I'm offering you a half-share in the universe!"
I love the way the Master's music plays in the background behind this speech. The Doctor refuses the offer, of course, and there is a further exchange as the Master asks him why.
"Why? Look at this. Look at all those planetary systems, Doctor. We could rule them all!"
"What for? What is the point?"
"The point is that one must rule or serve, that's a basic law of life. Why do you hesitate, Doctor? Surely it's not loyalty to the Time Lords, who exiled you on one insignificant planet?"
"You'll never understand, will you? I want to see the universe, not rule it."
This beautifully sets out their opposing philosophies, and in doing so more than makes up for the fact that the Master never got a proper introduction as a character back in Terror of the Autons - in a way his introduction occurs here, in his fourth story.
Only when the discussion reaches its end, and the Master moves to kill the Doctor, does the brain alien make his entrance. He challenges them both to justify their presence here, and by implication he is also testing the worthiness of their competing points of view. The brain alien explains that the weapon is the reason for their decline, because "the radiation from the weapon's power source poisoned the soil." This has been cleverly foreshadowed from early on in the story, as the reason why the colonists were having trouble growing their noms.
The Master finishes his argument by claiming that with the weapon they "could be gods." The brain alien, which has presumably already been living with the god-like power of the weapon for a long time, judges the Master unworthy to be a god. He demonstrates a fraction of god-like power when the Master tries to kill him, but he makes the Master's pewpewpew gun vanish. He gives the Doctor the option and ability to destroy the doomsday weapon, and the Doctor says
"Not only does justice prevail on your planet, sir, but also infinite compassion."
Destroying the weapon will also destroy the city, so the Doctor and the Master have to run away. When he sees some aliens running the wrong way the Doctor says
"Come back! You'll all be killed!"
The Master doesn't hesitate for the aliens but, oddly for someone who tries to kill the Doctor so often, he does pause long enough to say to the Doctor
"Come on! Do you want to die with them?"
They meet up with Jo and Caldwell and the four of them escape just ahead of a big explosion, as is traditional.
They are then immediately captured by Morgan and his henchmannys. Morgan is going to shoot the Doctor, the Master and Jo, but they are saved by the arrival of the not-ded-after-all colonists, leading to another gunfight which is won by Winton and the colonists. While this goes on the Master escapes back to his TARDIS and dematerialises out of the story.
Back at the dome, Winton tells the Doctor and Jo that only Ashe was blowed up inside the rocket. The Doctor's TARDIS has been found, so he and Jo can leave. Just before they do, we see Caldwell complete his character arc as he leaves his life with IMC behind and joins the colonists fully.
"Doctor, come back at once!"
The TARDIS reappears in the UNIT lab and it quickly becomes apparent to the Doctor and Jo that, from the Brigadier's point of view, this is still episode one and they have only been away for a few seconds.
"What are you two talking about?"
he asks them.
"Don't try and explain, Jo. He'd never understand."
Because the Brigadier has started on his own character arc - towards being a komedy character who's as thick as shit.
What's so good about Colony in Space?
As tempting as it is to say 'the Master' again, that can only be half the answer since he's only in half the story, lol! But certainly he is responsible for lifting the story from good to great, arriving just as the 'colonists vs IMC' plotline is flagging, and only he could take the role he does in part six, as the friend-enemy who offers the Doctor "a half-share in the universe" and means it.
The plot before the Master showed up was an interesting conflict between the arch-capitalists IMC, a personification of greed, and the colonists who want to escape from the lives they had on Earth to a simpler, Arcadian lifestyle. The writing leaves us in no doubt who are the baddys, since from before they even appear on screen the IMC mannys Dent and Morgan are willing to remorselessly murder colonists to get their way. This means that by the time Winton and some of the colonists fight back we know they are in the right to do so - helped, of course, by the Doctor being on their side.
Caldwell is the character caught in the middle, and the story is really his struggle to make the journey from siding with IMC in his pursuit of moneys to siding with the colonists because they aren't evil murdering baddys. This main thread barely interacts with the second plot about the Master and the alien city and its doomsday weapon (save for the bit about how the colonists were struggling to grow noms due to the weapon's radiation), so it is easy to see how this could have made for a story in its own right - I suggest that this would have really struggled to sustain six whole episodes though, seeing as it was already struggling by the time the Master did arrive partway through part four. Which leads us to...
Pertwee Six-Parter Padding Analysis
Colony in Space is the second Pertwee six-parter, and the first that finds it hard to justify the length. Unusually, the padding falls mainly in the first half of the story - perhaps because this is before the Master arrives, and it is always easier to disguise padding when the production team can throw in an entertaining Doctor-Master scene or the like.
The most visible sign of padding is in the back-and-forth between the colonists and IMC, as each side gets the upper paw over the other in turn, before fortunes are swiftly reversed. There is also the matter of the repetitious cliffhanger ends to parts one and two.
That's not to say the story isn't still great, however, with the final part (and especially its confrontation between the Doctor and the Master over the doomsday weapon) building to an epic-feeling conclusion. But it is best watched episodically, because if you try to watch the whole thing in a single session you will encounter the less-good first half, padding and all, before you get to the superior second half with the Master in it.
Oh, and that bit where the Brigadier repeats his line from part one... you wouldn't notice this if you didn't have the option of watching the whole story in one go, but it's a cheat: