Everything is set out nice and clear now, both from a plot perspective, but also the theme. We will start with the plot.
The Silurians ruled the Earth millions of years ago. They had an advanced civilization. One day, they detected a small planet on a collision course with the Earth, so they put their entire civilization into hibernation until the cataclysmic collision was over and the Earth’s atmosphere had stabilized. What they failed to account for was the Earth’s gravitational pull, which pulled the small planet into orbit rather than collision. The small planet became the moon. The Silurians slept. They are now waking up and many of them want their planet back. The Doctor has taken it upon himself to broker a peace between Silurians and humans because the alternative would be war. The Doctor is, ultimately, in a difficult position as neither side is entirely willing to trust him. He is alien, thus he may have sympathy for The Silurians. He looks like a human, therefore he may have sympathy for the humans.
This brings us to the theme. Doctor Who and The Silurians has quite a few thematic elements. As with most Doctor Who of this (and previous) eras, it has a strong Cold War element. You can read UNIT and the British government as a stand-in for The West, and The Silurians as a stand-in for the communist East. It can also be seen as a commentary about racism in an increasingly diverse Britain. The DVD includes a documentary called What Lies Beneath that unpacks quite a few ideas that permeate this story, intentionally or not. There is a lot to explore in this story, and I love that.