The 28-year-old suffered a horrific crash during a training ride in March that left him with a fractured spine, broken bones in his neck, broken ribs and a fractured sternum.
He spent much of the Spring in traction, barely able to move.
That he was able to return to competitive riding at all is a minor miracle, so to do so by the beginning of July underlines his desire to recover as much as the high standard of healthcare he received, for which he will be forever grateful to the NHS.
Yet the experience left him realising there is more to life than cycling.
And as the new year approaches, Thwaites has a decision to make - take a job outside of cycling, or continue in his bid to find a team and a ride in 2019.
“I’m motivated to race next year if the opportunity at a good team comes off,” Thwaites told The Yorkshire Post.
“I’d like to get back to racing, being motivated and happy that I’m cycling - but on a team that I enjoy being a part of is a huge part of it.
“If not, I am looking forward to new challenges outside of the sport, but cycling is where my heart is.
“In the end I just want to be happy with what I’m doing, especially after the accident, the main aim was being able to function in normal life again, to have a normal life outside, whether I cycle or not.
“There’s more to my life than cycling and I didn’t want cycling to take over. I also didn’t want to put too much pressure on myself to come back because my health was worth more than that.
“In terms of coming back to racing, it was all just a bonus really. The main thing was that I recovered from the injuries and that I was able to just be a normal person again.”
All through the months when he could barely move his body, his faith in his ability to get back on a bike rarely wavered, even in the darkest moments.
The support he received from doctors and British Cycling helped keep his spirits up.
“I did think that at some points I wouldn’t return... The doctors wouldn’t make any promises really because it was up in the air,” he recalled.
“It was a case of how well I responded to the surgeries and my rehabilitation. I think I was always fairly confident, and the surgeons were fairly confident, that I would be able to get back on a bike in some form but whether I’d be able to return to competitive racing at the same level was another question.
“But everything went really well and I had such a strong group of people around me. British Cycling helped out with a lot of the rehabilitation and that really helped.”
And when he got back on the bike, the old feelings came flooding back.
“It was just a great buzz to be back in the races. That’s what I love doing,” said Thwaites, in a statement that underlines how difficult a time he is having with the decision he has to make.
“It was always the challenge. I set my goal to get back to racing. I wasn’t too bothered about how the racing went and where I finished. It was just nice to get back to racing.”
An invite to a Great Britain cycling team ‘away day’ in Harrogate earlier this week, when Thwaites was one of a dozen or so riders who reconnoitred parts of the routes for next September’s UCI Road World Championships, also helped remind him of why he loves the sport so much.
Two huge races in his home county next year may also sway him, the world championships which he contested just months after completing the Tour de France last year, and next May’s Tour de Yorkshire.
“Next year’s route is probably easier than it has been,” said Thwaites at the route announcement yesterday which sees a start date of Thursday, May 2, in Doncaster and a race finish in Leeds three days later.
“There are three stages that should end in sprints, it’s just the last stage that will be very selective which is great. It means the winner is going to be a worthy winner because if you’re at the sharp end on that final day then you deserve to be up there.”