A powerful wave knocked him off balance, and he could only watch as the boat, still in gear, sailed away into the darkness without him.
He was wearing just shorts and a T-shirt in freezing Pacific water.
"The panic set in," he said. "This is a pretty heavy situation." An expert diver and experienced swimmer, he knew land was too far.
His only option was an offshore oil platform called Platform Gail, visible only as a faint glow in the blackness. He set off for it.
He pushed himself forward by thinking of his family. "I was devastating myself through my mind, just picturing my girls and my son growing up without me, and my wife not having a husband."
He kept telling himself: "Just keep swimming. You gotta get home to your family." Then he heard a splash.
"It was a medium-sized harbour seal. The seal would go underwater and he came up and nudged me, like a dog comes up and nudges your leg."
Thompson wrote in a blog post that the seal twice bumped him in the back of his legs with its nose when he stopped swimming and started treading water.
He began talking to it, singing it Grateful Dead songs and telling it jokes, which he said took his mind off his situation.
Five hours after entering the water, freezing and exhausted, he reached the platform.
"It started getting brighter and I'm just like, I'm crying. Shouting at the sky."
Crew aboard hauled him out, warmed him up, and called the Coast Guard. He was airlifted to hospital and treated for hypothermia.
The tow boat crew that later recovered his vessel said they couldn't believe he survived.
"Even putting on a wetsuit, being prepared, getting in that water, and swimming to that platform was horrendous," one crew member said.
“I can't imagine being in the water with shorts and a T-shirt at night. There was no moon. It was pitch black."
Thompson called the seal an angel. Nobody has ever offered a better explanation