We do have a chimney cap on top, but it's not entirely enclosed. Perhaps one of these days I'll take some hardware cloth and put it up around the top to prevent this from happening again.
Other than the grim discovery, the pipe cleaning went without a hitch. The pipe that is located inside of the house is a telescoping pipe. The screws were taken out of the middle of the pipe and the bottom end of the pipe was moved slightly up. A plastic bag was placed on the bottom of the pipe to catch creosote. Alex went on top of the roof with our wire chimney brush and pole. We connected a piece of rope to the other end of the brush. The pole that we purchased didn't reach all the way down the chimney. So when Alex was up brushing the top of the pipe, I grabbed the rope and pulled the brush down to get the bottom end.
Clean Chimney Pipe