The Black Death spread at the speed of trade. By sea it moved perhaps forty kilometres a day on Genoese and Venetian ships; over land, along the Silk Road, only about four. So a well-connected port fell fast even if it lay far from Sicily, while an isolated town nearby was spared. Connectivity, not distance, drew the death map.
Each city here is one well-mixed compartment — Susceptible, Infectious,
Recovered, Dead. A crowded port is a super-spreader node: its density raises the
local force of infection. Traffic on each route carries plague between cities, so busy lanes don't just
spread it wider — they burn each city harder, which is why choking the sea lanes lowers the
total dead.
The one medieval defence that worked was the Venetian quaranta giorni — forty days at anchor offshore. Seal a port and no plague crosses its harbour in either direction. Because the Atlantic North (Paris, London, Bruges) hangs off a single gateway at Bordeaux, one boom there can save a whole region.
Simplifications: the three plague forms — bubonic (summer fleas), pneumonic (winter coughs), and septicemic — are collapsed into one transmissibility. Deaths are a fixed case-fatality of the infected, not of the whole town, so a lightly-touched city loses few. This is the between-city story; within-city spread is the herd-immunity lab.
Something in the simulation stopped unexpectedly — the lesson continues without it. You can move on; nothing you did was wrong.