AFTER A WEEK AND A HALF, I left the fleet behind to head upriver, hoping to get a feel for what was happening beyond the chaos of the commercial fishery. I spent two weeks talking with locals, native leaders, and sportfishermen. Toward the end, Sean Magee, then Pebble's director of public affairs, invited me to join a media tour of the proposed mine site with five Alaska-based journalists, offering to take us up in a helicopter for a big-picture view.

"There's one of our drills there," he said, pointing out the window of the Bell 205 at a metal-lattice tower perhaps 40 feet tall, jutting up from a wooden platform on the tundra—one of the eight diesel-powered drill stations generating core samples. Later, we touched down on a ridge overlooking a bowl below Koktuli Mountain, the potential site of the open-pit mine. "We're not going to take it all," Magee said, explaining that the plans probably wouldn't call for extracting the entire resource. "There's going to be some smaller portion of it that makes sense."

From the helicopter, I had seen more of what I'd glimpsed on earlier bush flights around the region: an enormous expanse of tundra, pocked with lakes and ponds and paths worn into the spongy surface by migrating caribou herds. The dominant feature is the spider's web of creeks and rivulets slicing through the land like a child's scribble, the water wending its way through countless oxbows before joining larger streams. This is the final stretch of the sea-to-spawning gantlet, and the interconnectedness of the entire system was obvious.

The remarkable process by which salmon navigate back to their natal streams, arriving within a week or so of their parents four or five years earlier, relies heavily on smell. Metals or other pollutants could poison the fish and interfere with their homeward swim. Copper is of particular concern; a known toxin to the fish, it's capable of inhibiting their olfactory systems even at low levels. "In many respects, it's the water issues that are the most challenging from an engineering perspective," Magee told us in the town of Iliamna before we went out to the site. "If we can't protect the fish and the water and the wildlife, then we won't proceed with the project."

It was a nice assurance, if not entirely convincing, and one that I had heard several times before. Magee's 45-minute PowerPoint presentation hewed closely to the script that all Pebble officials seem to read from, and though I was impressed with the access and the openness, the visit yielded few revelations.

Situated 19 miles from the Pebble claim, Iliamna has about a hundred full-time residents. It used to be a sportfishing hotbed—its first lodge opened in the 1930s—but now, as the base of Pebble's exploratory operations, it's become something of a company town. The mining outfits had rented out most of the lodges and hotels to house the 92 people working on the exploration and the additional 60 or so consultants gathering data for the mine-permit reports.

I had visited Iliamna and several other native communities near Pebble prior to the mine-site tour. They are hardscrabble places with high unemployment and little funding for schools, health care, or other infrastructure. Winters are cold, and heating fuel—which, like most supplies, has to be flown or barged in at great cost—is expensive. Gas was $7.59 a gallon, and I had to promise one local elder a jerry can of unleaded for his boat before he'd talk to me.

It's a beautiful but harsh place, and it was easy to see why the town was losing population as young people went elsewhere. On the shores of the lake, I spent time with Myrtle Anelon, who was cutting up salmon at her family's fish camp, getting them ready for the smokehouse and canning. She described the town's embrace of the mine exploration—she and her husband own a building that the mining company is renting, and her daughter runs the Iliamna Development Corporation, which handles much of Pebble's local logistics—as keeping an open mind.