The city burned that same year. I assume the fire ended the plague.
This is up to intense debate. Most of the plague occurred in 1665, and it was peaking out in the spring of 1666. The fire came in early September of 1666....going on for roughly four days. The total area affected was about a mile by half-a-mile.
I get into this because I ended up discovering my original British family member left sometime in that summer of 1666 from London, shortly before the fire. They’d somehow survived the plague...got on the ship and left.