Fort Bragg, with a population of 7,000, is a ragged former timber town on the northern reaches of the California coast. It is in some ways the epitome of idealised small town America: the kind of town where any small happening is news, where the story of any event acquires a mythology almost before it happens.

When a blue whale was struck and killed offshore by the research vessel Pacific Star and drifted into an isolated cove just south of the city limits, she quickly acquired her own story and a name, The Whale, or The Smell, as my father started calling her when the stench of decay drifted into his nearby living room. He invited me over to smell for myself, but I politely declined the 10-minute drive.

News outlets were quick to pick up the story. Initial reports that she would be left to break down naturally were replaced by news that a team of volunteers, supervised by a Humboldt State University biologist, would section the body so that it could be winched up the cliffs. Local companies donated heavy equipment for the task, a composting facility offered to compost the blubber and enterprising local youths sold tickets to would-be spectators who came to gawk and left disappointed when they learned that the cove was in an inaccessible gated community.

Much to the relief of wealthy weekenders who quailed at the thought of having their ocean views replaced with a panorama of decaying whale, the removal effort went quickly. The blue whale is an endangered species, necessitating strict rules about the handling of remains, and the process was meticulously documented.

This narrative is captivating, but it is only one aspect of the story. Almost immediately, accusations of negligence on the part of the Pacific Star's crew emerged, with rampant speculation about the circumstances in which The Whale was struck. All evidence suggests that they did nothing wrong. In fact, the only reason we can confirm the cause of death is because the crew reported the incident, but it brings up a larger discussion about oceanographic research.

Fort Bragg is on a known whale migration route, and it's whale season. Some people questioned whether the Pacific Star should have been out at all, given the risk of whale strikes, and others wondered about the protocol observed by research vessels in waters frequented by whales. Ironically, the boat was on a surveying mission to update National Oceanic and Atmospheric Administration maps, which will be used to designate new marine protection areas.

This later proved to be another point of contention, with some whale advocates claiming that the echo sounding equipment used by the research vessel might have caused acoustic trauma that could have disorientated the animal. Fisheries advocates also protested at government interference in Fort Bragg's offshore waters, once one of the most productive marine ecosystems in the world, now heavily overfished. A cynic might say that the government should have stepped in before we fished to the brink of collapse.

This is the second ship strike and death to occur this year in California's waters, although we're still short of the record four deaths in 2007. Estimates on the number of blue whales left alive vary, but the numbers are low enough that any ship strike is a tragedy. These incidents have raised questions about the need to balance science with the creatures it is trying to save, and have illustrated the growing struggle over the right to use California's offshore waters: who has precedence? The whales, or the growing commercial, scientific, and recreational ship traffic?

Meanwhile, the whale's remains are buried in an undisclosed location in the forest, to let microbes do the work of cleaning the bones. Eventually, they will be mounted for display in a marine education facility which currently exists only in the imagination, much like the glory days of Fort Bragg's now moribund fishing and timber industries.

The smell still lingers.