"When I came to, I realized I was floating face down in the water, unable to move or feel anything below my shoulders," Theo St. Francis tells PEOPLE

In August 2013, all-star swimmer Theo St. Francis was preparing to study mechanical engineering at MIT. One late summer afternoon, the 18-year-old was testing submersible robots in the Boston Harbor with his freshman pre-orientation group when his life took a tragic turn.

“After lunch we were swimming in a designated swimming area and as I was entering the water from the beach — in about thigh-deep water — I dove forward and I hit something,” St. Francis tells PEOPLE. “I don’t know exactly what — could have been the bottom — but I immediately lost consciousness. When I came to, I realized I was floating face down in the water, unable to move or feel anything below my shoulders.”

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The nationally-ranked swimmer credits his skills in the water for saving his life. “I immediately knew that I had to get air and I think if it weren’t for the fact that I could breathe out of the side of my mouth from my swimming technique, I don’t know if I would have been able to.”

Theo was able to take sips of air out of the side of his mouth until waves washed him ashore where a lifeguard spotted him. He received emergency spinal fusion surgery in Boston with his family by his side.

“I still remember when [my family] entered the room and I saw the look on their faces — I knew something was really wrong,” he says.

Theo had broken his C6 vertebrae and was paralyzed from the shoulders down. He spent the next three months in the hospital before being transferred to inpatient rehab, where the doctor’s gave him a bleak prognosis.

“They warned me that I had an incomplete injury, meaning I could probably get some function back — but it certainly wouldn’t be enough to walk again — and I would probably need help for the rest of my life.”

As his peers began their freshman year of college, Theo began a rehab program to regain mobility at Spaulding Rehab Center at Massachusetts General Hospital.

“I was blessed to be at one of the most amazing spinal cord injury rehab hospitals in the country, if not the world, but in terms of the encouragement for continued recovery, there just isn’t an understanding of just how much farther someone can take their own healing,” he explains. “So, the process for me has been a lot of being able to recognize and discover those new ways that I was not shown in the beginning.”

One of the treatment methods Theo has found dramatically improved his condition is Pilates.

Theo says he was “blown away” when a trainer (who was once paralyzed herself) showed him a method of reconnecting the body through Pilates that worked for her.

“The medical system only really knows about [regaining mobility through] the preserved neural pathways,” he says. “They say, ‘Yeah, you’ll get some function back because you didn’t completely severe your spinal cord.’ But there isn’t an understanding in the medical system of just how complex the communication within the body is — and it’s that communication that the Pilates based approach has been able to help me with — to find new ways of connecting that I wouldn’t have ever gotten in a traditional medical treatment context.”

It has been just over two years since he was introduced to Pilates, and Theo has regained enough function to live independently, travel independently and stand and support himself on his own. He has even improved enough to ski, bike and return to his favorite place — the water. The now 22-year-old has already swam across Lake Tahoe on a relay team and is planning to swim the length of the Golden Gate Bridge in the future.

However, despite his advances, Theo says the traditional medical system doesn’t account for his progress.

“I was recently at a center where I was trying the exoskeleton and the physical therapist there did an exam on me,” he shares. “I was like, ‘This is kind of interesting, I haven’t had one of these since I was in the hospital, and that was a few years ago, we’ll just see what it’s like,’ and I kid you not, on that physical therapy exam, I hadn’t changed at all.

“The way that test measures function and strength and connection completely misses all of the progress I’ve made, which has been the progress that has enabled me to do all of these things I was told I would never do.”

The gap Theo sees in traditional spinal cord injury rehab has inspired him, along with his longtime trainer and now partner, Stephanie Behrendt, to launch Zebrafish Neuro, a redesigned approach to spinal cord injury rehab aimed at helping others recover from similar injuries. The two have launched a Kickstarter campaign to help in developing the second edition of their movement manual and hope to soon be able to share their work not only with Pilates teachers, but neuro-exercise therapists in specialty gyms around the world.

“With spinal cord injury rehab, there just is no protocol, there’s no guide book,”” he says. “The project that we’ve been working on is to make that guidebook, not because we have all the answers, but because there are things we know do work.”

Theo plans to continue spreading awareness about Pilates treatment in spinal cord injury when he returns to MIT this fall. Despite his setbacks, he holds an unwavering positive outlook on life and is more determined than ever.

“One of the things I’ve learned from this process is how to recognize that a process is unfolding and that what I know now is not an indicator of the way things will always be,” he says. “In the beginning, there was no way for me to know that I would get to the places I have – to find Pilates, to become independent in the way that I have.