Willcox said he tried to make nice with the guards, who he said recognized he posed no threat and looked after him well. But he was only allowed to meet with his lawyer after a month and allowed to call home once a month.
"We were really isolated, we really didn't know what was going on. We hardly saw each other enough to speculate," he said.
When he was being transported, he was locked in a wagon divided into pitch-dark partitions half the size of a phone booth. Some crewmembers reported being locked in for up to three hours.
Those months in jail, with no end visible and the threat of many more years in prison looming, provided much time for self-reflection.
Willcox is passionate about the environment and deeply fearful of the threat of climate change. He says even if he had known it would result in a two month jail sentence, he would still would have gotten on that boat.
But was it worth up to a decade and a half in prison? No way.
"This is a hugely important campaign. Climate change is huge. I am sincerely deeply worried about the future of my kids. But by the same token I'm not going to jail for 10 or 15 years over a demonstration," he said.
Earlier this month, Russian authorities announced the Greenpeace activists would be transferred to St Petersburg's notorious Kresty Prison, which holds the dubious distinction of being Europe's oldest.
The journey down from Murmansk, he said, was even more difficult than jail.
The activists were transported on an old prisoner train car where Willcox slept on a hard metal slab. His lawyer advised him to bring an empty bottle because they weren't allowed to go to the bathroom. The journey lasted days.
The one thing that kept him calm was the sound of the women's cell, which was right next to his.
"I'm just trying to not freak out, but the sound from the women's cell was this constant laughter, chatter, giggling, and carrying on and it's just like the greatest noise you can hear in your life," he recalled.
Finally, last week Willcox stood in the caged defendant's dock in a St. Petersburg courtroom for a five hour hearing that would determine his immediate fate. Most of the other crewmembers had been released on bail by that point and Willcox was hopeful.
But as the judge began speaking, Willcox's interpreter recited the reasons he should be denied bail. His heart sank, convinced that he, the captain, was being made the example. Then, the judge listed the reasons why he should be allowed bail and motioned that it was granted.
"It was just a perfect example of the whole two months," he said. "You're up, you're down. You're up, you're down and you don't know what's going on."
Willcox is not yet a free man.
Though prosecutors have backed off the piracy charges, he still faces charges of hooliganism which carry a maximum jail term of seven years.
"You keep telling yourself, I know it's not going to go like that, I know I'm going to be out one month, two months, six months. I know this can't go on, but it's going on. It's still going on," he said.
He's still hoping to be released soon, hoping perhaps the spotlight of the Winter Olympics, which Russia will host in Sochi in February, will encourage authorities to release him and his fellow activists.
His wife is applying for a visa to visit him, but he's not losing any time in case the worst comes. After being denied contact for most of the past two months, they speak on the phone twice a day.
Willcox hopes he'll be released soon. He's already planning his next mission.
"I'm ready to get back to work," he said.
Another Greenpeace boat, the Rainbow Warrior, is scheduled to sail up the East Coast of the United States early next year. Willcox hopes to be on board.