The limies weren't even that big into the spice trade, it was the dutch. You mention nutmeg, nutmeg and cloves came from a certain string of small indonesian islands only. There were some english traders there, when the dutch were trying to monopolize the trade.

The dutch sent a delegation, that angered the natives that killed them. The dutch came back and exterminated the natives. Killed every single one of them, and the english and other traders there.

Edit: Adaman islands if memory serves, fuzzy on the years no time to look up.