UPDATE on 10/23/09: From the San Francisco Chronicle – "Two World War II cargo ships moored among Benicia's fabled "ghost fleet" since the late 1940s will be towed out of Suisun Bay next month, scrubbed clean in dry dock and ultimately sent to Texas to be broken up and sold for scrap".

Read more about the clean-up effort in the Chronicle here.

On the surface of the story, the Ghost Fleet of Suisun Bay (commonly called the "Mothball Fleet" but most accurately referred to as the Suisun Bay National Defense Reserve Fleet) is leaking toxic waste in the form of peeling ship paint containing nasty heavy metals into an already stressed bay ecosystem. Bad guys: Mothball Fleet. Good guys: Enviros who are suing. Simple, right?

But when we began digging into the story, we found the origins of the problem and current impasse to be a bit more convoluted. I'll attempt to quickly summarize: The fleet has been there since the 1940's. It wasn't until 2006 that it came to light that the exterior paint is peeling from the ships and falling into the bay. Many tons of toxic heavy metals have already fallen into Suisun Bay and there's a lot more to be had. Oddly enough, the story was initially triggered by a study that was commissioned by the federal body who oversees the fleet, the Department of Transportation's Maritime Administration, or MARAD for short. So the Contra Costa Times got a hold of a draft of that report and now, the ships are at the center of a different kind of battle long after they've been decommissioned.

Environmental groups (NRDC, Arc Ecology and San Francisco Bay Keeper), community leaders and water regulators justifiably want MARAD to either remove or better maintain the ships so that they are not polluting these waters that serve as both fishing and nursery grounds for several fragile or threatened species. That includes humans who are often out there catching fish for dinner. Historically, MARAD has been regularly removing and dismantling the ships but like most federal bodies whose charter was drafted during WWII, alacrity is not at the top of their mission statement.

Check out a larger map of the fleet

The real issue now seems to be that MARAD has had to completely stop removing ships because they can't clean their hulls of potentially hazardous invasive biological species (to comply with the U.S. Coast Guard's National Aquatic Invasive Species Act of 2003) without scraping more paint into the bay. So, until someone develops a system to clean the hulls that doesn't scrape more paint into the water, the San Francisco Regional Water Quality Control Board says that MARAD can't remove the ships.

The one possible solution that everyone pretty much agrees upon is to dismantle the ships locally so that they don’t have to be cleaned of invasive species. There are currently no ship dismantlers operating on the West Coast but there's a company called Allied Defense Recycling located on Vallejo's Mare Island Naval Shipyard that's chomping at the bit to tear those ships apart. But they've also run into red tape. And while they await permits and approvals from multiple parties, the ships continue to rot and pollute.

It's always easier to write a story with clear heroes and villains. But to me, it does seem that MARAD, environmental groups and water regulators all agree that we have a problem that must be addressed. So, what now? I guess we wait. Perhaps this lawsuit will kick start some aspect of the clean-up process but in the meantime, frustration mounts for all parties involved and many pointing index fingers are suffering from overuse.

Watch the "Ghost Fleet" TV Story online, as well as find additional links and resources. Also, check out the online photo set of the ships and behind the scenes images.

You may listen to the "Cement – A Dirty Business" Radio report online, as well as find additional links and resources. Also don't miss our behind-the-scenes photos for this story.

Amy Standen is a Reporter for QUEST and Radio News at KQED-FM.