After learning that a storm was headed for Isla Nublar, Owen went to the raptor paddock to check on the raptors. It was already raining when he arrived, though, and because of the rain, he slipped and fell into the raptor paddock. He wasn't injured, but he couldn't get out of the paddock, and decided to stay with the raptors in a shelter he'd built for them until the storm was over. However, a clap of thunder startled the raptors once Owen was in the shelter, and they all scattered, one of them cutting Owen's leg. He tried to crawl out then, but since the logs on the shelter were wet, they collapsed, and knocked Owen unconscious.
Over an hour later, Owen finally woke up and tried to get out from under the logs. He couldn't, though, and ended up spraining his left wrist. In the following hour, Owen continued to try and fail to get himself out. After an hour of continuous labor, though, he was still stuck, and exhaustion took over, leaving him to pass out in the flood water on the ground. He didn't drown, though, as the raptors pulled him out of the water to keep him from drowning.
During the time Owen was stuck under the log, Blue, the Beta of the raptor pack, headed to get help. She managed to dig herself out of the paddock, then ran to the bungalow and found Alexia, Owen's wife. Once she found the blonde, she took her back to the raptor paddock, and the two pulled Owen into a building to keep him safe. There, he woke up just long enough to let Alexia know that he was alive, then passed out again.