Literally, the quote is describing what London looks like outside the window of Mr. Utterson's home, where he sits by the hearth with his friend Mr. Guest. The passage is saying that the city is covered ("drowned") in fog, which would not be uncommon for London. All that can be seen is the glow of the many (at this time) gas lamps around London that look to Utterson like pustules or pus-filled boils under human skin. Beneath the fog, though he can't see anything, he can hear the sounds of London, which reassure him the life of the great city is going on. Traffic through the arteries (main roads) of the city sounds like a great wind.
As a literary device, this passage is an example of the pathetic fallacy , which is when weather and/or landscape reflect the emotional mood of a character. This London scene mirrors the grim,...
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confused mood of Utterson as he contemplates Hyde as a possible murderer and his old friend Jekyll's connection with this evil man. He has just confirmed what he feared from Jekyll's will, which is that Hyde has been planning to murder Jekyll.
This is an elaborate and atmospheric description of London during the late Victorian era. London was notoriously foggy—a fog which we now know to have been a result of air pollution caused by industry and the lack of controls placed on fossil fuels. This fog often makes an appearance in Gothic novels, a visual representation of the obfuscation and confusion which are key themes in Gothic literature (and in this novel in particular). Here, Stephenson personifies the London fog, stating that it "slept" above the city which seemed "drowned" beneath it. The impression this creates is of a city wreathed in fog as if in water, struggling to breathe. The city, too, is personified through the use of this language.
The lamps of the city are glimmering "like carbuncles," large stones just visible through the "muffle and smother" of the fog. Stephenson's reference to the fog as "fallen clouds" suggests that it has descended from the skies to be something other, language which cannot help but recall the idea of beings having "fallen" from heaven—something once angelic, which has now become demonic. The fog is smothering the city: we can understand this fog to be a visual representation of the city's sin and secrets, which is crushing the life out of it. The life of the town is still rolling in on roads described as "arteries," supplying critical life blood to the city's body, but the fog, not the life, creates the primary impression of this city.
This quote shows up in Chapter 5: "The Incident of the Letter." What the author is trying to do by writing these lines is (in my opinion) to describe the city and to do so in a way that makes it seem spooky and ominous.
First of all, there is the idea that the city is drowned -- that the fog is somehow smothering and choking and muffling it. All of those images show the fog having a negative effect.
The word "carbuncle" can mean either a jewel or a disgusting looking abscess/boil on your skin. I think Stevenson means the latter -- that the lamps are just glowing dully and looking unhealthy through the fog.,
So, to me, he's just trying to make it seem very oppressive in the fog-covered city. I believe Stevenson is trying to do this to convey how much of an effect Hyde's evil has on the characters in the story.