Long story is long!
The Silurians capture the Doctor and pewpewpew a UNIT manny on their way out. Their hypno-eye even tidies up after them, by closing up the tunnel. While it seems there is nothing they can't do with this extra eye, and mannys have thumbs, cats are still best.
Captain Hawkins sees the UNIT manny and draws his gun quick as a flash. He also sees a big mark left on the wall where the Silurians' tunnel had been made and unmade. Liz also sees the wall, and that the Doctor is gone, and the mess that got made when he got pewpewpewed - the Silurians forgot to use their hypno-eyes on that!
Captain Hawkins tells the Brigadier the Silurians have been in their base killing their d00dz, and about the "scorch mark on the wall." They leap into action at once, leaving Liz to try to sort out the Doctor's still-secret formula.
After putting him in the big cage, Pink Face and his friend talk to the Doctor. He tells them he has cured the plague, and learns from them that Green Face has been killed when Pink Face gloats.
"Our leader is dead. I killed him. I am the leader now."He likes saying that.
Liz tells the no-longer-secret formula to a doctor (another not the Doctor) so they can make it to cure all the infected mannys. Like the proper baddys that they are, Pink Face and his friend already have a new plan to wipe out all the mannys, which they are happy to discuss in front of the Doctor because, as I said, they are proper baddys.
For it to work they need POWER (a Ben Steed episode, so easily enough to wipe out any and all mannys it comes into contact with), and to get it they plan to make the Doctor turn the nuclear reactor back on.
The Brigadier and Liz are luckily standing on the right bit of the set when the Silurians remake their tunnel into the research centre (it's not as good as the original). They get captured, but the Silurians don't know about Captain Hawkins, who was just out of sight.
Pink Face is about to kill the Brigadier when Captain Hawkins heroically attacks, but he gets pewpewpewed.
This is by far the biggest misstep of Doctor Who and the Silurians, killing off Captain Hawkins like that. In terms of the plot structure, it makes sense that an important character such as Captain Hawkins should die to show that the Silurians mean business and inspire the Doctor to stop trying to make peace with them and to resist them, but hasn't that already been shown by all the mannys they have killed so far, and the two attempts to wipe out all the mannys? As we shall soon see, the Doctor still has not learned that lesson, and never will - unless that is what Peter Davison's Doctor meant when he said "There should have been another way," i.e. they never should have killed off Captain Hawkins.
What it does mean is that, while the Sylvester McCoy era of Doctor Who saved its best story until last, the Jon Pertwee era has already peaked and only at his second story. As a captain, had Hawkins lived, he could have filled the role that Mike Yates would later play in 'the UNIT family,' only infinitely cooler and a much more plausible love interest for Jo Grant... as well as for any cats that happened to show up.
The Silurians burst into the cyclotron room and start pewpewpewing the extras (the Doctor having persuaded them to spare the regular characters after Captain Hawkins's death). Jon Pertwee is really good in these dramatic, climactic scenes, although they are missing a certain Paul Darrow-shaped something to make them truly excellent.
There is a large dump of exposition delivered to explain how the Silurians' superweapon works, but it is cleverly divided between the Silurian, the Doctor, and Liz, with the Brigadier there to ask the questions, and this stops the scene from getting bogged down.
The Doctor is, of course, only pretending to go along with the baddys' plan, which Liz recognises. Despite her telling the Brigadier to "trust him," even she is shocked when she finds out what he plans on doing. The superweapon starts to glow to show that it is beginning to go, but then the Doctor and Liz turn the POWER to maximum and the full force of Gunn Sar's moobs and Ben Steed's sexism causes the superweapon to explode!
The Doctor tells the Silurians
"The reactor is now permanently overloaded. There's going to be a massive explosion, and a colossal radiation leakage."Pink Face and his friends leave the mannys behind to go back to their base for some sleeps and to wait for the radiation to go away. Pink Face says of the mannys
"They will all stay here to die from the radiation."
In their base, one of the Silurians has to stay awake to let the others have their sleeps, and that one will be killed when the centre blows up - showing a first and only glimpse of some nobility, Pink Face accepts the responsibility as leader. He tells his friend that when they next wake up in 50 years (even Dragon is impressed by how much sleeps Silurians have!) his friend will be the new leader.
The Brigadier thinks the Doctor was bluffing and they are safe really, but then the Doctor says it is real and they should all leave as fast as they can - but the Brigadier knows they are trapped in there.
The Doctor tries to jury-rig the nuclear reactor to shut it down safely, perhaps in the hopes that it will turn off the Blakes 7 DVD. He says
"I'll try fusing the control of the neutron flow."which doesn't sound quite right, somehow.
But it works, and in the next scene the Doctor has gone straight back to the Silurian base. Pink Face comes in and tries to pewpewpew the Doctor, but the Brigadier runs in and shoots him repeatedly until he falls over. The Doctor says
"There's a wealth of scientific knowledge down here, Brigadier, and I can't wait to get started on it."
and the Brigadier gives him a look that says 'you're a dick.' Clearly he remembers what happened with Dr Quinn, even if the Doctor doesn't.
Back at the cyclotron set, the Brigadier waits for the Doctor and Liz to leave and then says to Corporal Nutting (who could easily have been Captain Hawkins if they hadn't stupidly killed him off already)
"Give them time to get clear, and then set off those explosive charges. I want that Silurian base sealed permanently."
In the Silurian base we see that Pink Face still isn't ded yet, but after he stands up he is alarmed by the camera shaking a lot, like he's on the bridge of the Enterprise, and then he gets blown up.
The Doctor and Liz are on location in Bessie when they see some explosions. The Doctor immediately realises what has happened and says
"But that's murder! They were intelligent alien beings. A whole race of them. And he's just wiped them out."
Er, yes, but... I mean... when has that ever stopped you, Doctor, either before or after this? You do remember that they just tried to wipe out all the mannys twice and killed Captain Hawkins on top of that? And how do you know they have been wiped out and not just buried in their beds where they are having nice long sleeps?
The Doctor has jumped to some hasty conclusions here, and all because he got along well with Green Face, his Autloc. Doctor, you failed to save a civilisation, but at least you helped one Silurian.
What's so good about Doctor Who and the Silurians?
Paul Darrow is in it. Purr purr purr, that's good enough for me.