How could you do this to me? You answer me.

Sometimes I think there's merit to the theory that Larys is a literal rat king who's in the walls because there was a rat lurking around during Rhaenyra's small council meeting-

And one was lurking behind the throne when Rhaenyra was holding court with the smallfolk-

But ultimately I think that much like the hints that Alys Rivers is skinchanging her owl and the Black Philip of Harrenhal, it will never be confirmed and will just be something fun you can buy into if you want.

The point of the ever-present rats is thematic and foreshadowing of not only Rhaenyra's downfall but the dragon-wielding dynasty as a whole ('the dying of the dragons'). The Targ dynasty will live on post Dance but the height of their power will be behind them and the dragons will be all but extinct. This is the first fell blow that starts their slow dwindling. From gods to ordinary men and women to… gone. (Until Daenerys, a Targaryen trying to use her dragons to do some good in the world instead of just going to grab power for herself.)

This quote from the rat feast in S3.E3 is relevant:

Also these quotes from Mysaria:

There is no power but what the people allow you to take. [S1.E9]

And [S2.E5]:

Also this exchange between Rhaenyra and Mushroom in Fire & Blood:

Rhaenyra: They are vermin. Drunks and fools and gutter rats. One taste of dragonflame and they will run. Mushroom: Drunks they may be, but a drunken man knows not fear. Fools, aye, but a fool can kill a king. Rats, that too, but a thousand rats can bring down a bear. I saw it happen once, down there in Flea Bottom.

Like the rats in the Red Keep, the smallfolk of King's Landing crawl for crumbs while trampled under the feet of the ruling class. The royals and highborn have been ignoring, looking down on, oppressing, mistreating, starving and exploiting the smallfolk since forever. They feel entitled to do this and never consider that the smallfolk are suffering, might one day turn on them or that they could pose a serious threat to them.

Now that Rhaenyra is queen there seem to be more rats than ever in the Red Keep and they're much bolder than ever before. The smallfolk are becoming increasingly desperate and disaffected because the war, the food shortages, the blockade, the instability, etc. are driving them to the brink. Desperate people become willing to risk their own lives to do something bold and reckless if it might fill their bellies or bring them restitution. Something bold like... storming the pit and trying to bring down the beasts that have been used to subjugate them. (Of course there's also the question of who the the real beasts are: the dragons or those who wield them to their benefit and others' detriment?)

Mysaria is on Rhaenyra's council and she's working to uplift the smallfolk. Hope of a better life is being held up to them (I do think Mysaria is sincere in wanting to help them) but ultimately it will be yanked away from them because the Crown is broke and Rhaenyra will have to focus on securing her throne and dealing with her enemies. When the smallfolk realize Rhaenyra's reign is not bringing the salvation they've hoped for and things only get worse for them yet again, it will be the straw that breaks the camel's back.

The rats in the Red Keep have been there for generations and it's a problem that's been getting worse for several regimes, at least since the reign of Viserys. Several rulers have failed to deal with the issue. Rhaenyra is not the only highborn who's wronged the smallfolk, but everything will come to a head during her reign.

Helaena said she's scared of the rats. But it wasn't rats who came to murder her son; it was rat catchers sent by a dragon. The (gutter) rats haven't come to eat the rich yet.

(gif is mine)

Another Helaena quote is relevant. Young Helaena said her millipede 'has eyes but I do not believe it can see.' The millipede's body represents the Targaryens of the Dance and the fact that they've been blind to what they've wrought. The only thing that can bring down the house of the dragon is itself.

There's also Helaena's comment after Jaehaerys has died-

So many focus on the fact that Helaena seems to be downplaying the death of her son while missing the point made - maybe it's being made clumsily but it stands nonetheless. The smallfolk were expected to show sympathy and outrage that a royal prince had been murdered, but do the royals care or try to help when smallfolk children die in similarly horrible ways? In her own strange way Helaena was trying to hold empathy for the smallfolk. True selfless empathy for the lowborn is something we rarely see amongst the highborn and royals. The death of another 'forgotten' child haunts the narrative in Season 2: Hugh and Cat's daughter. A lowborn child died from illness and starvation caused by the blockade and the nobles hoarding food. She was one of many. (And Helaena and Hugh have both been carrying on and trying to make the best despite their devastating loss but eventually they'll both snap.)

The ruling class have been killing each other to sit on a chair of swords while the lowborn have been dying for a crust of bread. The dragons dance and the Targaryens have been playing their game of thrones oblivious to the fact that their future downfall was beneath their feet. They've been looking up when they should've been looking down to places like Flea Bottom.

The way Alys Rivers talks about Harrenhal constantly passing between highborn hands while none of them cherish it has parallels to the way the throne (i.e. control of the realm) passes through hands. What is the realm if not the people who inhabit it (ALL the people including the poor and lowborn and downtrodden?) And who in the high seats cherishes them or does right by them?

ALICENT & RHAENYRA

“And the queen knew nothing of it?” “They hated me from the start. Resented my influence, my mere presence. My own father kept their plot from me.”