The men allegedly attacked him when he went back to a Banff, Alberta, hotel after a New Year's Eve party, the Canadian Broadcasting Group reported.
"They came out and dragged me into their room and pulled me into the toilet and three men just continued to punch me in the head and in the body," McDonald said. "And so I kind of just scrambled to get out of the hotel."
McDonald, who began the 4,349-mile journey in March, left his bag in the room.
The bag contained his hard drive, wallet and all the video of his journey -- which he hopes to use to inspire others to press on with fundraising.
"When I couldn't see it, it was heart wrenching. My whole world came apart."
But someone returned the bag to McDonald, who said he is thankful to retrieve the footage.
As a child, McDonald was hospitalized for a rare spinal condition. He has now run 180 marathons to raise money for children's hospitals, and has about 20 to go.
He has raised about $100,000 so far.
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